Re: [gmx-users] Umbrella sampling of peptide-membrane system

[Mijiddorj B]

Dear John,

Thank you very much for your advice.

Best regards,
Mijiddorj

Hi,
>
> Justin's tutorial is not a fully generalized procedure for umbrella
> sampling; it shows a workflow for one specific example which is not always
> applicable to other systems.
>
> In general, you don't have to use position restraints for anything in
> umbrella sampling. Justin uses them to keep the fibril in place for
> specific reasons, as noted in the paper he based the tutorial on.
>
> That said, what are you trying to do? Adding restraints to the bilayer is
> probably a bad idea, seeing as how the motion of the bilayer is an
> important physical behavior.
>
> Are you calculating the PMF for a molecule traversing a lipid bilayer? If
> so, there are many examples in the literature that detail a procedure
> that's probably much more relevant to you.
>
> Best,
>
> John
>
>
>
> > Dear GMX users,
> >
> > I would like to ask about position restraint during the umbrella
> sampling.
> > 1. Is it need to make position restraint of lipid bilayer during the
> > umbrella sampling simulation?
> > 2. The position restraint was used for the B chain of amyloid-beta
> > peptides
> > in prof. Justin's tutorial. Can I run the simulations without position
> > restrain of lipid molecules in the case of lipid bilayer?
> > or
> > 3. Can I use the position restraint for only phosphorus atoms of the
> > headgroups of both leaflets?
> >
> > If you have any experience, please let me advise which one is better for
> > this kind of calculation.
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> send
> > a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
>
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Re: [gmx-users] Umbrella sampling of peptide-membrane system

[John Whittaker]

Hi,

Justin's tutorial is not a fully generalized procedure for umbrella
sampling; it shows a workflow for one specific example which is not always
applicable to other systems.

In general, you don't have to use position restraints for anything in
umbrella sampling. Justin uses them to keep the fibril in place for
specific reasons, as noted in the paper he based the tutorial on.

That said, what are you trying to do? Adding restraints to the bilayer is
probably a bad idea, seeing as how the motion of the bilayer is an
important physical behavior.

Are you calculating the PMF for a molecule traversing a lipid bilayer? If
so, there are many examples in the literature that detail a procedure
that's probably much more relevant to you.

Best,

John



> Dear GMX users,
>
> I would like to ask about position restraint during the umbrella sampling.
> 1. Is it need to make position restraint of lipid bilayer during the
> umbrella sampling simulation?
> 2. The position restraint was used for the B chain of amyloid-beta
> peptides
> in prof. Justin's tutorial. Can I run the simulations without position
> restrain of lipid molecules in the case of lipid bilayer?
> or
> 3. Can I use the position restraint for only phosphorus atoms of the
> headgroups of both leaflets?
>
> If you have any experience, please let me advise which one is better for
> this kind of calculation.
>
> Best regards,
>
> Mijiddorj
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.
>


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Re: [gmx-users] Umbrella sampling with restraint on the center of mass of ligand

[Justin Lemkul]

On 1/15/20 6:32 AM, gmx user1 wrote:

Dear GMX users

I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00624 ;
https://www.sciencedirect.com/science/article/pii/S0005273615004319?via%3Dihub
)

Yet, I am not certain of which .mdp settings I should use to accomplish my
goal, the documentation is not clear and most infomation I find
refers to the application of harmonic potentials when the reaction
coordinate is a distance between two groups.


If you're not clear what the published method is or how to reproduce it, 
I suggest you contact the corresponding author and ask for sample input 
files.



Here are my .mdp settings:

pull= yes
pull_print_com  = yes
pull_print_ref_value= yes
pull_nstxout= 500
pull_nstfout= 0
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 1
pull_coord1_geometry= direction-periodic
pull_coord1_vec = 0 0 1
pull-coord1-origin  = 0 0 0
pull_group1_name= LIG
pull_coord1_groups  = 0 1
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.0   ; restrain in place
pull_coord1_k   = 500  ; kJ mol^-1 nm^-2

Essentially, I created a vector between the center-of-mass of the ligand
and an absolute reference (0,0,0) and I had to use pull_coord1_geometry =
direction-periodic ( instead of direction) ,because the simulation crashed.
This also forces me to perform an NVE simulation.

Is this the right way of applying a an harmonic restraint on the
center-of-mass of a ligand for umbrella sampling? Are these settings
correct?


If you're looking at ligand translocation across a membrane, you should 
not be using (0,0,0) as a reference. The conventional reaction 
coordinate is the normal to the bilayer, so the reaction coordinate 
connects the COM of the bilayer with the COM of the ligand along the z-axis.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Umbrella Sampling on Lipid Bilayers, Pulling Issue and Umbrella Sampling Window Simulation Issues.

[Justin Lemkul]

On 11/1/19 2:09 PM, Alexander Phillips wrote:

Hello Everyone,

I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid
in Water. I also have a single vitamin E in the mixture aswell (inside of
the POPC bilayer). I am trying to perform umbrella sampling by pulling the
vitamin E and measuring it's binding energy to POPC. I am basing most of my
work off of the tutorial made by Justin Lemkul. The plan for my umbrella
sampling is to pull the vitamin E vertically out of the membrane  (from the
center of the membrane to some distance into the water). However I am
having issues with performing umbrella sampling. I believe the issue is one
of two things (or perhaps a mixture of both):
1) The simulation where I pull the Vitamin E out of POPC is happenning too
quickly and I cannot gather enough frames to get valid input windows for
the umbrella sampling portion.
2) The umbrella sampling portion is not keeping the Vitamin E around the
starting portion and it falls back into the membrane.

I will attach the mdp files I used for both, and hopefully someone can give
me some advice about how to do this / fix it.


It may be a combination of things. Your pull rate is quite fast and your 
force constant is very small. I suggest experimenting with slower 
pulling and/or a stiffer spring constant.



I am running in Gromacs 4.6.5 so a few things are changed from the files
given in Justin's tutorial, however I believe ultimately it's about the
same.


Any reason to use such antiquated software? The modern versions will be 
MUCH faster (and are actually supported by the developers in case of 
problems).


-Justin


Here is the mdp for the Pulling:


integrator = md
dt= 0.03
nsteps   = 25
nstcomm  = 10

comm-grps  =
nstxout = 5000
nstvout = 5000
nstfout  = 5000
nstlog= 1000  ; Output frequency for energies to log file
nstenergy = 100   ; Output frequency for energies to energy file
nstxtcout  = 1000  ; Output frequency for .xtc file
xtc_precision   = 5
xtc-grps =

energygrps   = Lipids Solvent PULLING_ATOC
nstlist  = 10
ns_type   = grid
pbc  = xyz
rlist   = 1.4
coulombtype= Shift  ;Reaction_field (for use with Verlet-pairlist) ;PME
(especially with polarizable water)
rcoulomb_switch  = 0.0
rcoulomb   = 1.2
epsilon_r= 15   ; 2.5 (with polarizable water)
vdw_type= Shift  ;cutoff (for use with Verlet-pairlist)
rvdw_switch  = 0.9
rvdw= 1.2  ;1.1 (for use with Verlet-pairlist)

tcoupl = v-rescale
tc-grps= Lipids Solvent PULLING_ATOC
tau_t= 1.0  1.0 1.0
ref_t = 310 310 310
Pcoupl= parrinello-rahman
Pcoupltype= semiisotropic
tau_p   = 12.0 12.0 12.0 ;parrinello-rahman is more stable
with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4 3e-4
ref_p= 1.0 1.0 1.0

gen_vel   = no
gen_temp   = 310
gen_seed= 473529

constraints = none
constraint_algorithm  = Lincs
continuation  = no
lincs_order  = 4
lincs_warnangle  = 30

; Pull Code
pull = umbrella
pull-geometry = direction-periodic
pull-start = yes
pull-nstxout = 10
pull-nstfout = 10
pull-ngroups = 1
pull-group0 = Lipids
pull-group1 = PULLING_ATOC
pull-vec1 = 0 0 1
pull-rate1 = 0.01
pull-k1 = 20




 End of MDP
1 ---

The second MDP file (the one used for the Umbrella Sampling production run)
is listed here

integrator = md
dt= 0.002
nsteps   = 1000
nstcomm  = 10
comm-grps   =

nstxout  = 5
nstvout  = 5
nstfout   = 5000
nstlog = 1000  ; Output frequency for energies to log
file
nstenergy  = 5000  ; Output frequency for energies to energy
file
nstxtcout   = 5000  ; Output frequency for .xtc file
xtc_precision= 100
xtc-grps =
energygrps   = Lipids Solvent PULLING_ATOC

nstlist= 5
ns_type = grid
pbc= xyz
rlist= 1.4

coulombtype   = Shift  ;Reaction_field (for use with Verlet-pairlist)
;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb  = 1.2
epsilon_r   = 15   ; 2.5 (with polarizable water)
vdw_type  = Shift  ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw   = 1.2  ;1.1 (for use with Verlet-pairlist)

tcoupl= v-rescale
tc-grps   = Lipids Solvent PULLING_ATOC
tau_t   = 1.0  1.0 1.0
ref_t  

Re: [gmx-users] Umbrella sampling on lipid bilayer

[John Whittaker]

> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
> them.

Hi,

Justin replied in this mail:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html

Best,

John

>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
>
> I made my protein-membrane system with charmm-gui.
>
> so my force is charmm36.
>
> I used the equilibration input files that charmm-gui provide ,
>
> and run 400 ns simulation for equilibration of my system .
>
> RMSD , temperature and pressure is good , so I think my system is stable .
>
> Every thing is good until I use following pull code in my mdp file .
>
> The bilayer does not move and the ligand passes through the membrane
>
> But over time , the length of the z axis increases , and
>
> 4 water molecules are also separated from the membrane.
>
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
> [image: Mailtrack]
> 
> Sender
> notified by
> Mailtrack
> 
> 09/29/19,
> 06:33:51 PM
> --
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Re: [gmx-users] Umbrella sampling on lipid bilayer

[Justin Lemkul]

On 9/25/19 5:50 AM, Mahsa Rezaei wrote:

Dear Dr. Warren

Thanks for your response .

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane .


Distortion of membrane protein systems (elongation or compaction along 
the z-axis) with CHARMM is a bug that was recently fixed. You can either 
patch the code with the fix found at 
https://gerrit.gromacs.org/c/gromacs/+/13297 or wait for the next 
release in any of the 2018, 2019, or 2020 branches and re-run your 
simulations.


-Justin


Thank you .

Regards

Mahsa.



Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052dallas.warren at monash.edu

-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 24 Sep 2019 at 19:50, Mahsa Rezaei https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:


* Dear gromacs users,

*>>* I am using following pull code in md simulation
*>* for pulling a ligand across the plasma membrane model.
*>* Ligand passes through the membrane,but along simulation,
*>* the size of axis z increases.
*>* My size box is 8.52807   8.52807  14.0.
*>* And the pull distance is less than one-half the length of the box vector
*>* along.pull distance is 6 nm.
*>* After simulation my size box is 8.09025   8.09025  91.84508.
*>* What should I do?
*>>* I would be very appreciated for your such kind helps.
*>>* My mdp file  :
*>* title   = Umbrella pulling simulation
*>* ; Run parameters
*>* integrator  = md
*>* dt  = 0.002
*>* tinit   = 0
*>* nsteps  = 30 ; 600 ps
*>>* ; Output parameters
*>* nstlog  = 1000
*>* nstxout = 500   ; every 1 ps
*>* nstvout = 500
*>* nstfout = 500
*>* nstxtcout   = 500; every 1 ps
*>* nstcalcenergy   = 500
*>* nstenergy   = 500
*>* ; PME electrostatics parameters
*>* coulombtype = pme
*>* ; Single-range cutoff scheme
*>* cutoff-scheme   = Verlet
*>* nstlist = 20
*>* rlist   = 1.2
*>* rcoulomb= 1.2
*>* vdwtype = Cut-off
*>* vdw-modifier= Force-switch
*>* rvdw_switch = 1.0
*>* rvdw= 1.2
*>* ; Berendsen tempearture coupling is on in two groups
*>* tcoupl  = nose-hoover
*>* tc_grps = Protein_LIG TIP3_CLA DOPC
*>* tau_t   = 1.01.0   1.0
*>* ref_t   = 303.15 303.15 303.15
*>* ; Pressure coupling is on
*>* pcoupl  = Parrinello-Rahman
*>* pcoupltype  = semiisotropic
*>* tau_p   = 5.0
*>* compressibility = 4.5e-5  4.5e-5
*>* ref_p   = 1.0 1.0
*>* refcoord_scaling= com
*>* ; Bond parameters
*>* constraints = h-bonds
*>* constraint_algorithm= LINCS
*>* continuation= yes
*>* ;
*>* nstcomm = 100
*>* comm_mode   = linear
*>* comm_grps   = Protein_LIG TIP3_CLA DOPC
*>* ; Generate velocities is off
*>* gen_vel = no
*>* ; Periodic boundary conditions are on in all directions
*>* pbc = xyz
*>>* ; Pull code
*>* pull= yes
*>* pull_ncoords= 1 ; only one reaction coordinate
*>* pull_ngroups= 2 ; two groups defining one reaction
*>* coordinate
*>* pull_group1_name= BILAYER
*>* pull_group2_name= LIG
*>* pull_coord1_type= umbrella  ; harmonic potential
*>* pull_coord1_geometry= direction
*>* pull_coord1_dim = N N Y
*>* pull_coord1_vec = 0 0 1
*>* pull_coord1_groups  = 1 2
*>* pull_coord1_start   = yes   ; define initial COM distance > 0
*>* pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
*>* pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
*>* pull_nstxout= 500; every 1 ps
*>* pull_nstfout= 500; every 1 ps
*>>>* [image: Mailtrack]
*>* <
*>* 

Re: [gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear Dr. Warren
Unfortunately,I missed your reply!

Thanks for your response .

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane .

Thank you .

Regards

Mahsa




[image: Mailtrack]

Sender
notified by
Mailtrack

09/25/19,
03:36:23 PM

On Tue, Sep 24, 2019 at 1:20 PM Mahsa Rezaei 
wrote:

> Dear gromacs users,
>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_dim = N N Y
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
>
> [image: Mailtrack]
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Re: [gmx-users] Umbrella sampling on lipid bilayer

[Dallas Warren]

Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 24 Sep 2019 at 19:50, Mahsa Rezaei 
wrote:

> Dear gromacs users,
>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_dim = N N Y
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
>
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Re: [gmx-users] Umbrella sampling PMF using pull-geometry=direction

[Pradyumn Sharma]

I am sorry I forgot to give the link in the last mail.

https://indianinstituteofscience-my.sharepoint.com/:f:/g/personal/pradyumn_iisc_ac_in/EkAdkzcZsepHvbE1UDJPS5UBg2mENMYsRC2S0Z2DDWS9xQ?e=3GeICo

On Fri, May 17, 2019 at 5:03 PM Pradyumn Sharma <
cherpradyumnsha...@gmail.com> wrote:

> Dear all
> I am trying to get a PMF for a small molecule translocation through an
> asymmetric membrane. I am doing it using pull-geometry= direction to do
> umbrella sampling at each window. I am getting a profile in which PMF of
> molecule in the bulk water at one side of the membrane is different from
> the one in bulk water on the other side, which should not be the case
> because it is bulk water on both sides. I saw the trajectory, as well as my
> density map, both shows that windows at either end are corresponding to the
> position of molecule in bulk water.
> I am giving a link for files related including:
>
> a. MDP file - for one window
> b. Density map for water along the z-direction, where 0 represents my
> membrane centre
> c. PMF profile
>
> Am I interpreting this correctly? if some mistake is there in parameters
> or my interpretation kindly let me know.
>
> Additional details:
> 1. I am using gromacs-2018.2.
> 2. I got the initial system. from CHARMMGUI.
> 3. Proper overlapping is there I checked my histograms, also if that was
> the case than PMF would not have been so smooth.
> 3. I already did US simulations for symmetric membrane with
> pull-geometry=distance, also I have reproduced results in the literature
> already.
> --
> Regards
> Pradyumn Sharma
> PhD Student
> Department of Chemical Engineering
> Indian Institute Of Science (IISc)
>


-- 
Regards
Pradyumn Sharma
PhD Student
Department of Chemical Engineering
Indian Institute Of Science (IISc)
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Re: [gmx-users] Umbrella Sampling - Changing force constant values between samples

[Justin Lemkul]

On 10/22/18 1:45 PM, Dan Gil wrote:

Hello,

I am wondering if it is valid to use different force constant (k) values
between samples for umbrella sampling.

It seems that gmx_wham accepts different k values in a set, but I wanted to
make sure this is OK. Should I be wary of any artifacts with these
simulations?


People do this all the time. I can't think of anything unexpected that 
would happen.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 7/6/18 10:42 AM, hosein geraili wrote:

Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash script to 
create the summary_distances.dat, but the problem is at first I would get the error 
"Unknown command-line option -o", then I used -oh instead of -o which worked, 
but the problem is the summary_distances.dat file is not correct, and it seems like:


-oh produces a histogram, not the distances themselves. Use -oall. I 
have fixed the script in the tutorial. Sorry for the typo.


-Justin


0 1 2 3 4 5 6 7 8 9 10 11 ...265 1000.000266 1000.000267 1000.000268 1000.000269 1000.000270 1000.000271 1000.000272 1000.000273 1000.000274 1000.000275 1000.000276 1000.000277 1000.000278 1000.000279 1000.000...10 tail -n 1 dist${i}.xvg | awk "{print 
$2}"11 tail -n 1 dist${i}.xvg | awk "{print $2}"12 tail -n 1 dist${i}.xvg | awk "{print $2}"13 tail -n 1 dist${i}.xvg | awk "{print $2}"14 tail -n 1 dist${i}.xvg | awk "{print $2}"15 tail -n 1 dist${i}.xvg | awk 
"{print $2}"16 tail -n 1 dist${i}.xvg | awk "{print $2}"17 tail -n 1 dist${i}.xvg | awk "{print $2}"18 tail -n 1 dist${i}.xvg | awk "{print $2}"19 tail -n 1 dist${i}.xvg | awk "{print $2}"20 tail -n 1 
dist${i}.xvg | awk "{print $2}"21 tail -n 1 dist${i}.xvg | awk "{print $2}"22 tail -n 1 dist${i}.xvg | awk "{print $2}"23 tail -n 1 dist${i}.xvg | awk "{print $2}"24 tail -n 1 dist${i}.xvg | awk "{print $2}"25 
tail -n 1 dist${i}.xvg | awk "{print $2}"26 tail -n 1 dist${i}.xvg | awk "{print $2}"27 tail -n 1 dist${i}.xvg | awk "{print $2}"...172 1000.000173 1000.000174 1000.000175 1000.000176 1000.000177 1000.000178 1000.000179 
1000.000180 1000.000181 1000.000182 1000.000183 1000.000184 1000.000185 1000.000...
What is the problem?Best


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Umbrella Sampling - Pulling distance larger 0.49 times box size Error during NPT equilibration

[Justin Lemkul]

On 7/4/18 6:51 AM, Chenlin Lu wrote:

Dear gromacs users,


Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out 
of a protein channel. Basically, I followed the procedure given by Justin's 
tutorial. The configuration generation was finished correctly and the .mdp file 
summary_distance.txt are shown below:

pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Protein
pull_group2_name= AU
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= direction  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_vec = 0 0 -1


This is unlikely to be a viable reaction coordinate. Beware copying too 
closely from the tutorial; it has very unique geometry and 
considerations. Likely you're getting "random" movement because the 
chosen biasing potential is ineffectual.


-Justin


pull_coord1_rate= 0.01
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0
​
0.000 3.220
1.000 3.242
2.000 3.264
3.000 3.354
4.000 3.302
... ...
396.000 0.186
397.000 0.175
398.000 0.179
399.000 0.170
400.000 0.185

The problem is when I am doing NPT equilibration (the .mdp file is the same as 
before expcet the pull rate is zero) I got a mistake which says pulling 
distance is larger than 0.49 times box size. So I checked the trajectory which 
shows the Au ion moves randomly and out of box. The point is the coordinate of 
Au ion changes significantly and doesn't along the pull direction (the movement 
direction is vertial with the pull direction). It is supposed to be in a 
neighbourhood of the specified distance, isn't it? Why would this happen?  
Could anybody help me?

Thanks,
Chenlin

--

Chenlin Lu

Department of Chemical Engineering,

Tsinghua University, Beijing, 100084

Tel: 86-13120180517

Email: luc...@mails.tsinghua.edu.cn



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Umbrella sampling: window distance - harmonic force constant

[Hermann, Johannes]

Okay. Thanks Justin!


On 27.03.2018 21:12, Justin Lemkul wrote:



On 3/27/18 4:44 AM, Hermann, Johannes wrote:

Dear All, dear Justin,

I am playing around with my umbrella sampling setup and I was looking 
at your paper which you linked in your umbrella sampling tutorial 
("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using 
Molecular Dynamics").
Up to a distance of 2nm you use a 0.1nm spacing, beyond a 0.2nm 
spacing. Which harmonic force constant pull_coord1_k do you use for 
the 0.1nm spacing? In comparison to the 0.2nm spacing, where 
pull_coord1_k=1000.
Is there a general rule of thumb between window distance and force 
constant? Or is it always try and error while checking the histograms?


You can set the value of k based on experimental methods or somewhat 
ad hoc, but then yes, you have to check overlap. I don't know of any 
useful way of trying to predict how the intermolecular forces in the 
system will respond in such a way that you can exactly say a priori 
how to set up the windows.


-Justin



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] Umbrella sampling: window distance - harmonic force constant

[Justin Lemkul]

On 3/27/18 4:44 AM, Hermann, Johannes wrote:

Dear All, dear Justin,

I am playing around with my umbrella sampling setup and I was looking 
at your paper which you linked in your umbrella sampling tutorial 
("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using 
Molecular Dynamics").
Up to a distance of 2nm you use a 0.1nm spacing, beyond a 0.2nm 
spacing. Which harmonic force constant pull_coord1_k do you use for 
the 0.1nm spacing? In comparison to the 0.2nm spacing, where 
pull_coord1_k=1000.
Is there a general rule of thumb between window distance and force 
constant? Or is it always try and error while checking the histograms?


You can set the value of k based on experimental methods or somewhat ad 
hoc, but then yes, you have to check overlap. I don't know of any useful 
way of trying to predict how the intermolecular forces in the system 
will respond in such a way that you can exactly say a priori how to set 
up the windows.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

[Rose]

Check the size of pullf-umbrellaX files(in a directory which gmx WHAM use 
them). MAYBE you refer for example a wrong pullf-umbrella0 file 
unintentionally. It happened to me.
Check the size, they should be almost close to each other.

Sent from my iPhone

> On Mar 14, 2018, at 18:14, Ben Tam  wrote:
> 
> Dear all,
> 
> I have a rather strange problem. Currently I am trying to get a PMF of a 
> water molecule through a hydrophobic materials. At the end of using "gmx 
> wham", I get a rather good histogram and it cover the whole range of the 
> system. However at the making profile.xvg. I get the answer "nan" inside the 
> file. Therefore I really cannot think of why is it giving me that?
> 
> Currently I set it as :
> ;Pull code
> pull = yes
> ;pull-cylinder-r = 0.5
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = SOL
> pull_group2_name = MOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = direction-periodic ; simple distance increase, 
> direction-periodic
> pull_coord1_vec = 1 1 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y Y Y
> pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 1 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
> 
> Also this appears when I used the command "gmx wham":
> 
> Switched to exact iteration in iteration 1
>   1) Maximum change -1.00e+20
> Converged in 2 iterations. Final maximum change -1e+20
> 
> Therefore I really don't understand what I have to do in order to get a 
> profile.xvg. I understand the k value is high, but without that high value, 
> the water won't settle within the assign window.
> 
> Am I doing something wrong? because I got a good histogram but no result in 
> the profile.xvg? Thank you very much for your help.
> 
> Best regards,
> 
> Ben
> 
> 
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Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

[Jochen Hub]

Am 14.03.18 um 16:26 schrieb Ben Tam:

Hi Neha,

I have tried that, I have reduced the number of reaction coordinate (from 42 to 10 
windows) and still it gives me "nan". I have check each specific pullf.xvg and 
pullx.xvg, there are non zero value inside. Hence forth I don't understand what else 
going on.

Hi Mark,

Okay I will do that. However what file should I need to attach with the issue?

Thank you both for your answer. However I have one more question. When using gmx wham, it 
is either pullf.dat or pullx.dat are need to provide. As far as I know, you need the 
force act upon the position of the molecules. What I don't understand is, why do I only 
need to provide pullx or pullf but not both? how does "gmx wham" understand at 
what position that the force is applied or vice versa?  is it because it read it off .tpr?


WHAM needs the position, which can (obviously) be taken from pullx, but 
the position can also be computed from pullf when you know the force 
constant (since F = -k*dx). In doubt, I would always use pullf, since 
they files are usually smaller so reading is faster. Parsing pullf files 
is also much easier (so less bug-prone).


Please check your histograms carefully, do they really well overlap? You 
could also play with gmx wham -min -max. This can help to take out 
single data points in the first or last histograms (very right or very 
left) that are "disconnected" from the histograms.


Hope this helps,
Jochen



Thank you very much,

Ben

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Awasthi, Neha 
<neha.awas...@biologie.uni-goettingen.de>
Sent: Wednesday, March 14, 2018 15:16
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in 
profile

Before labeling this as a bug and reporting on redmine, I suggest you try :


1) calculate the profile over part(s) of your reaction coordinate, i.e. reduce 
the number of windows you work with.

In other words,  start with small number of windows in pullx-files.dat & 
tpr-files.dat.

If you get partial profiles, it would point towards some windows (along your 
reaction coordinate) that cause problems.  One needs to patiently test 
increasing number of windows.


2) A small region of poor overlap can lead  to profiles with nan.

high k value should not be a problem provided you have the required number of 
windows and the histograms overlap (check about how much overlap is good 
overlap) . Sometimes, along a steep profile, histograms are difficult to 
assign, and tend to shift leading to small regions of poor overlap.


Hope this helps.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham 
<mark.j.abra...@gmail.com>
Sent: Wednesday, March 14, 2018 3:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in 
profile

Hi,

That would generally suggest something divided by zero, or similar, eg
because no data was in a histogram bin, etc.

That behavior is a bug that we could perhaps fix if you would be so kind as
to report it at https://redmine.gromacs.org.

But the core problem remains that something about how you sampled didn't
meet the expectations of gmx wham.

Mark

On Wed, Mar 14, 2018, 15:45 Ben Tam <btam...@hotmail.co.uk> wrote:


Dear all,

I have a rather strange problem. Currently I am trying to get a PMF of a
water molecule through a hydrophobic materials. At the end of using "gmx
wham", I get a rather good histogram and it cover the whole range of the
system. However at the making profile.xvg. I get the answer "nan" inside
the file. Therefore I really cannot think of why is it giving me that?

Currently I set it as :
;Pull code
pull = yes
;pull-cylinder-r = 0.5
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = SOL
pull_group2_name = MOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = direction-periodic ; simple distance increase,
direction-periodic
pull_coord1_vec = 1 1 1
pull_coord1_groups = 1 2
pull_coord1_dim = Y Y Y
pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

Also this appears when I used the command "gmx wham":

Switched to exact iteration in iteration 1
1) Maximum change -1.00e+20
Converged in 2 iterations. Final maximum change -1e+20

Therefore I really don't understand what I have to do in order to get a
profile.xvg. I understand the k value is high, but without that high value,
the water won't settle within the assign window.

Am I doing something wrong? because I got a good histogram but no result
in the profile.xvg? Thank you very much for yo

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

[Ben Tam]

Hi Neha,

I have tried that, I have reduced the number of reaction coordinate (from 42 to 
10 windows) and still it gives me "nan". I have check each specific pullf.xvg 
and pullx.xvg, there are non zero value inside. Hence forth I don't understand 
what else going on.

Hi Mark,

Okay I will do that. However what file should I need to attach with the issue?

Thank you both for your answer. However I have one more question. When using 
gmx wham, it is either pullf.dat or pullx.dat are need to provide. As far as I 
know, you need the force act upon the position of the molecules. What I don't 
understand is, why do I only need to provide pullx or pullf but not both? how 
does "gmx wham" understand at what position that the force is applied or vice 
versa?  is it because it read it off .tpr?

Thank you very much,

Ben

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Awasthi, Neha 
<neha.awas...@biologie.uni-goettingen.de>
Sent: Wednesday, March 14, 2018 15:16
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in 
profile

Before labeling this as a bug and reporting on redmine, I suggest you try :


1) calculate the profile over part(s) of your reaction coordinate, i.e. reduce 
the number of windows you work with.

In other words,  start with small number of windows in pullx-files.dat & 
tpr-files.dat.

If you get partial profiles, it would point towards some windows (along your 
reaction coordinate) that cause problems.  One needs to patiently test 
increasing number of windows.


2) A small region of poor overlap can lead  to profiles with nan.

high k value should not be a problem provided you have the required number of 
windows and the histograms overlap (check about how much overlap is good 
overlap) . Sometimes, along a steep profile, histograms are difficult to 
assign, and tend to shift leading to small regions of poor overlap.


Hope this helps.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham 
<mark.j.abra...@gmail.com>
Sent: Wednesday, March 14, 2018 3:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in 
profile

Hi,

That would generally suggest something divided by zero, or similar, eg
because no data was in a histogram bin, etc.

That behavior is a bug that we could perhaps fix if you would be so kind as
to report it at https://redmine.gromacs.org.

But the core problem remains that something about how you sampled didn't
meet the expectations of gmx wham.

Mark

On Wed, Mar 14, 2018, 15:45 Ben Tam <btam...@hotmail.co.uk> wrote:

> Dear all,
>
> I have a rather strange problem. Currently I am trying to get a PMF of a
> water molecule through a hydrophobic materials. At the end of using "gmx
> wham", I get a rather good histogram and it cover the whole range of the
> system. However at the making profile.xvg. I get the answer "nan" inside
> the file. Therefore I really cannot think of why is it giving me that?
>
> Currently I set it as :
> ;Pull code
> pull = yes
> ;pull-cylinder-r = 0.5
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = SOL
> pull_group2_name = MOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = direction-periodic ; simple distance increase,
> direction-periodic
> pull_coord1_vec = 1 1 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y Y Y
> pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 1 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> Also this appears when I used the command "gmx wham":
>
> Switched to exact iteration in iteration 1
>1) Maximum change -1.00e+20
> Converged in 2 iterations. Final maximum change -1e+20
>
> Therefore I really don't understand what I have to do in order to get a
> profile.xvg. I understand the k value is high, but without that high value,
> the water won't settle within the assign window.
>
> Am I doing something wrong? because I got a good histogram but no result
> in the profile.xvg? Thank you very much for your help.
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing l

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

[Awasthi, Neha]

Before labeling this as a bug and reporting on redmine, I suggest you try :


1) calculate the profile over part(s) of your reaction coordinate, i.e. reduce 
the number of windows you work with.

In other words,  start with small number of windows in pullx-files.dat & 
tpr-files.dat.

If you get partial profiles, it would point towards some windows (along your 
reaction coordinate) that cause problems.  One needs to patiently test 
increasing number of windows.


2) A small region of poor overlap can lead  to profiles with nan.

high k value should not be a problem provided you have the required number of 
windows and the histograms overlap (check about how much overlap is good 
overlap) . Sometimes, along a steep profile, histograms are difficult to 
assign, and tend to shift leading to small regions of poor overlap.


Hope this helps.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham 
<mark.j.abra...@gmail.com>
Sent: Wednesday, March 14, 2018 3:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in 
profile

Hi,

That would generally suggest something divided by zero, or similar, eg
because no data was in a histogram bin, etc.

That behavior is a bug that we could perhaps fix if you would be so kind as
to report it at https://redmine.gromacs.org.

But the core problem remains that something about how you sampled didn't
meet the expectations of gmx wham.

Mark

On Wed, Mar 14, 2018, 15:45 Ben Tam <btam...@hotmail.co.uk> wrote:

> Dear all,
>
> I have a rather strange problem. Currently I am trying to get a PMF of a
> water molecule through a hydrophobic materials. At the end of using "gmx
> wham", I get a rather good histogram and it cover the whole range of the
> system. However at the making profile.xvg. I get the answer "nan" inside
> the file. Therefore I really cannot think of why is it giving me that?
>
> Currently I set it as :
> ;Pull code
> pull = yes
> ;pull-cylinder-r = 0.5
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = SOL
> pull_group2_name = MOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = direction-periodic ; simple distance increase,
> direction-periodic
> pull_coord1_vec = 1 1 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y Y Y
> pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 1 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> Also this appears when I used the command "gmx wham":
>
> Switched to exact iteration in iteration 1
>1) Maximum change -1.00e+20
> Converged in 2 iterations. Final maximum change -1e+20
>
> Therefore I really don't understand what I have to do in order to get a
> profile.xvg. I understand the k value is high, but without that high value,
> the water won't settle within the assign window.
>
> Am I doing something wrong? because I got a good histogram but no result
> in the profile.xvg? Thank you very much for your help.
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

[Mark Abraham]

Hi,

That would generally suggest something divided by zero, or similar, eg
because no data was in a histogram bin, etc.

That behavior is a bug that we could perhaps fix if you would be so kind as
to report it at https://redmine.gromacs.org.

But the core problem remains that something about how you sampled didn't
meet the expectations of gmx wham.

Mark

On Wed, Mar 14, 2018, 15:45 Ben Tam  wrote:

> Dear all,
>
> I have a rather strange problem. Currently I am trying to get a PMF of a
> water molecule through a hydrophobic materials. At the end of using "gmx
> wham", I get a rather good histogram and it cover the whole range of the
> system. However at the making profile.xvg. I get the answer "nan" inside
> the file. Therefore I really cannot think of why is it giving me that?
>
> Currently I set it as :
> ;Pull code
> pull = yes
> ;pull-cylinder-r = 0.5
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = SOL
> pull_group2_name = MOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = direction-periodic ; simple distance increase,
> direction-periodic
> pull_coord1_vec = 1 1 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y Y Y
> pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 1 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> Also this appears when I used the command "gmx wham":
>
> Switched to exact iteration in iteration 1
>1) Maximum change -1.00e+20
> Converged in 2 iterations. Final maximum change -1e+20
>
> Therefore I really don't understand what I have to do in order to get a
> profile.xvg. I understand the k value is high, but without that high value,
> the water won't settle within the assign window.
>
> Am I doing something wrong? because I got a good histogram but no result
> in the profile.xvg? Thank you very much for your help.
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 3/3/18 9:27 AM, rose rahmani wrote:

Sorry, i can't understand, what do you mean"-zprof0" option? Could you
please give me an example?


Please read the gmx wham help information for a description.

-Justin


On 3 Mar 2018 16:47, "Justin Lemkul"  wrote:



On 3/3/18 7:02 AM, rose rahmani wrote:


Hi

I use umbrella sampling to calculate PMF, for studying the interaction of
different aminoacids with nanosheet separately. But at the minimum distance
from sheet, potential is zero for all PMF diagrams. I mean there isn't any
positive potential even at closest distance of aminoacid from sheet. I did
pulling and sampling manyyy times with different rates ...,still the same
problem... how could it be possible?What is the problem? I really get
confused. There isn't any closer distance to sample it.
Would you please help me?


WHAM works by assigning the leftmost (lowest index) window a free energy
value of zero, and then constructs the rest of the profile relative to it.
You can adjust this with the -zprof0 option.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Umbrella sampling

[rose rahmani]

Sorry, i can't understand, what do you mean"-zprof0" option? Could you
please give me an example?

On 3 Mar 2018 16:47, "Justin Lemkul"  wrote:



On 3/3/18 7:02 AM, rose rahmani wrote:

> Hi
>
> I use umbrella sampling to calculate PMF, for studying the interaction of
> different aminoacids with nanosheet separately. But at the minimum distance
> from sheet, potential is zero for all PMF diagrams. I mean there isn't any
> positive potential even at closest distance of aminoacid from sheet. I did
> pulling and sampling manyyy times with different rates ...,still the same
> problem... how could it be possible?What is the problem? I really get
> confused. There isn't any closer distance to sample it.
> Would you please help me?
>

WHAM works by assigning the leftmost (lowest index) window a free energy
value of zero, and then constructs the rest of the profile relative to it.
You can adjust this with the -zprof0 option.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 3/3/18 7:02 AM, rose rahmani wrote:

Hi

I use umbrella sampling to calculate PMF, for studying the interaction of
different aminoacids with nanosheet separately. But at the minimum distance
from sheet, potential is zero for all PMF diagrams. I mean there isn't any
positive potential even at closest distance of aminoacid from sheet. I did
pulling and sampling manyyy times with different rates ...,still the same
problem... how could it be possible?What is the problem? I really get
confused. There isn't any closer distance to sample it.
Would you please help me?


WHAM works by assigning the leftmost (lowest index) window a free energy 
value of zero, and then constructs the rest of the profile relative to 
it. You can adjust this with the -zprof0 option.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] umbrella sampling

[Rose]

Oooh, i mean roomMate :)))

Would you please answer my questions?

Sent from my iPhone

> On Feb 5, 2018, at 0:48, Rose  wrote:
> 
> 
> Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, 
> but i have some problems in my gmail which i can't open my emails every 
> times(i don't why but it's sth related to country ip&...) because Of that i 
> have to use my roomate account,soy again
> 
> 
> Sent from my iPhone
> 
>> On Feb 5, 2018, at 0:35, Justin Lemkul  wrote:
>> 
>> 
>> I don't know whether you're intentionally changing your email address or 
>> display name, but please refrain from doing so as it is very confusing who 
>> I'm talking to.
>> 
>>> On 2/4/18 4:00 PM, Nick Johans wrote:
>>> maybe this is irrelative but i expeienced in pulling that when i decrease
>>> dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
>>> comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
>>> crushed before(when dt=2fs)  so i had had to decrease nsteps or decrease
>>> pull_rate , but i don't face with these crush anymore! i can pull it too
>>> close. i know maybe these beginner confessions seem unacceptable ; and
>>> silly.
>>> i know this question is not accurate and can have many answers but, as a
>>> professional and experienced person, would you please tell me, whenever you
>>> face with  a crushed simulation, what will  you check?doubt? in your
>>> system(separate of anything related to cpu& computers limitations) .
>>> what cause simulations to be crushed usually?
>> 
>> If your simulation is crashing, you're doing something inappropriate, by 
>> causing particles to collide with one another. This is an entirely separate 
>> issue from the relationship between constraints and time step, dt. Your 
>> simulations are not unstable because of excessively fast bond vibrations, 
>> they're unstable because the nonbonded interactions in your system are 
>> unfavorable when allowed to run with dt = 2 fs.
>> 
>> If the system is unstable at any point, you should verify the 
>> parametrization of any non-standard species, which in your case is the 
>> sheet. I recall long ago telling you this would be a challenging entity to 
>> parametrize, yet you quickly obtained a model and began using it. What 
>> verification did you perform to assure yourself that interactions of this 
>> ZnS sheet are reasonable in the context of protein moieties? Did you perform 
>> any QM interaction energies? Are there experimentally known binding free 
>> energies for model compounds? How do you know this model is appropriate?
>> 
>> These are all things you need to consider, and questions that are not within 
>> the scope of this mailing list.
>> 
>> -Justin
>> 
 On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul  wrote:
 
 
> On 2/4/18 3:25 PM, Rose wrote:
> 
> Jeah,i meant grompp :)))
> and last question, i set constraint = h-Bonds, and dt=0.002 because Of
> that(since usually h-Bonds have Max frequency and if i assume them
> constraint so it's not reasonable to set dt=0.001 ) , is this assumption
> true?
 You can always decrease dt, that's "reasonable," but it makes no sense and
 is inefficient. Without any form of constraints, you'd likely be limited to
 dt = 0.0005 in many cases.
 
 
 -Justin
 
 Sent from my iPhone
>> On Feb 4, 2018, at 23:30, Justin Lemkul  wrote:
>> 
>> 
>>> On 2/4/18 1:56 PM, Rose wrote:
>>> Thank you so much,
>>> Is it difference between using gmx tpbconv -extend  5ps OR use .gro
>>> file of last simulation as an input For new 5nS
>>> simulation?(continiuation=yes in .mdp file)
>> The only reason to invoke grompp is if you're changing something about
>> the system. For a simple continuation use tpbconv/convert-tpr and mdrun
>> -cpi.
>> 
>> -Justin
>> 
>> Sent from my iPhone
 On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:
 
 
> On 2/2/18 10:44 AM, Rose wrote:
> Sent from my iPhone
> 
>> On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
>> 
>> 
>>> On 2/2/18 8:43 AM, rose rahmani wrote:
>>>  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and
>>> 4nS
>>> simulation for each window.
>>> 
>>> g_energy -f umbrella0.edr -o out.xvg
  1  Bond 2  Angle3  Proper-Dih.  4
>>> Improper-Dih.
>>>   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
>>> Coulomb-(SR)
>>>   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
>>> Kinetic-En.
>>>  13  Total-Energy14  Conserved-En.   15  Temperature 16
>>> Pressure
>>> 
>>>  17  Constr.-rmsd18  Vir-XX  19 

Re: [gmx-users] umbrella sampling

[Rose]

Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, but 
i have some problems in my gmail which i can't open my emails every times(i 
don't why but it's sth related to country ip&...) because Of that i have to use 
my roomate account,soy again


Sent from my iPhone

> On Feb 5, 2018, at 0:35, Justin Lemkul  wrote:
> 
> 
> I don't know whether you're intentionally changing your email address or 
> display name, but please refrain from doing so as it is very confusing who 
> I'm talking to.
> 
>> On 2/4/18 4:00 PM, Nick Johans wrote:
>> maybe this is irrelative but i expeienced in pulling that when i decrease
>> dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
>> comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
>> crushed before(when dt=2fs)  so i had had to decrease nsteps or decrease
>> pull_rate , but i don't face with these crush anymore! i can pull it too
>> close. i know maybe these beginner confessions seem unacceptable ; and
>> silly.
>> i know this question is not accurate and can have many answers but, as a
>> professional and experienced person, would you please tell me, whenever you
>> face with  a crushed simulation, what will  you check?doubt? in your
>> system(separate of anything related to cpu& computers limitations) .
>> what cause simulations to be crushed usually?
> 
> If your simulation is crashing, you're doing something inappropriate, by 
> causing particles to collide with one another. This is an entirely separate 
> issue from the relationship between constraints and time step, dt. Your 
> simulations are not unstable because of excessively fast bond vibrations, 
> they're unstable because the nonbonded interactions in your system are 
> unfavorable when allowed to run with dt = 2 fs.
> 
> If the system is unstable at any point, you should verify the parametrization 
> of any non-standard species, which in your case is the sheet. I recall long 
> ago telling you this would be a challenging entity to parametrize, yet you 
> quickly obtained a model and began using it. What verification did you 
> perform to assure yourself that interactions of this ZnS sheet are reasonable 
> in the context of protein moieties? Did you perform any QM interaction 
> energies? Are there experimentally known binding free energies for model 
> compounds? How do you know this model is appropriate?
> 
> These are all things you need to consider, and questions that are not within 
> the scope of this mailing list.
> 
> -Justin
> 
>>> On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul  wrote:
>>> 
>>> 
 On 2/4/18 3:25 PM, Rose wrote:
 
 Jeah,i meant grompp :)))
 and last question, i set constraint = h-Bonds, and dt=0.002 because Of
 that(since usually h-Bonds have Max frequency and if i assume them
 constraint so it's not reasonable to set dt=0.001 ) , is this assumption
 true?
>>> You can always decrease dt, that's "reasonable," but it makes no sense and
>>> is inefficient. Without any form of constraints, you'd likely be limited to
>>> dt = 0.0005 in many cases.
>>> 
>>> 
>>> -Justin
>>> 
>>> Sent from my iPhone
> On Feb 4, 2018, at 23:30, Justin Lemkul  wrote:
> 
> 
>> On 2/4/18 1:56 PM, Rose wrote:
>> Thank you so much,
>> Is it difference between using gmx tpbconv -extend  5ps OR use .gro
>> file of last simulation as an input For new 5nS
>> simulation?(continiuation=yes in .mdp file)
> The only reason to invoke grompp is if you're changing something about
> the system. For a simple continuation use tpbconv/convert-tpr and mdrun
> -cpi.
> 
> -Justin
> 
> Sent from my iPhone
>>> On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:
>>> 
>>> 
 On 2/2/18 10:44 AM, Rose wrote:
 Sent from my iPhone
 
> On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
> 
> 
>> On 2/2/18 8:43 AM, rose rahmani wrote:
>>   Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and
>> 4nS
>> simulation for each window.
>> 
>> g_energy -f umbrella0.edr -o out.xvg
>>>   1  Bond 2  Angle3  Proper-Dih.  4
>> Improper-Dih.
>>5  LJ-146  Coulomb-14   7  LJ-(SR)  8
>> Coulomb-(SR)
>>9  Coul.-recip.10  COM-Pull-En.11  Potential   12
>> Kinetic-En.
>>   13  Total-Energy14  Conserved-En.   15  Temperature 16
>> Pressure
>> 
>>   17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20
>> Vir-XZ
>> 
>>   21  Vir-YX  22  Vir-YY  23  Vir-YZ  24
>> Vir-ZX
>> 
>>   25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28
>> Pres-XY
>> 

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

I don't know whether you're intentionally changing your email address or 
display name, but please refrain from doing so as it is very confusing 
who I'm talking to.


On 2/4/18 4:00 PM, Nick Johans wrote:

maybe this is irrelative but i expeienced in pulling that when i decrease
dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
crushed before(when dt=2fs)  so i had had to decrease nsteps or decrease
pull_rate , but i don't face with these crush anymore! i can pull it too
close. i know maybe these beginner confessions seem unacceptable ; and
silly.
i know this question is not accurate and can have many answers but, as a
professional and experienced person, would you please tell me, whenever you
face with  a crushed simulation, what will  you check?doubt? in your
system(separate of anything related to cpu& computers limitations) .
what cause simulations to be crushed usually?


If your simulation is crashing, you're doing something inappropriate, by 
causing particles to collide with one another. This is an entirely 
separate issue from the relationship between constraints and time step, 
dt. Your simulations are not unstable because of excessively fast bond 
vibrations, they're unstable because the nonbonded interactions in your 
system are unfavorable when allowed to run with dt = 2 fs.


If the system is unstable at any point, you should verify the 
parametrization of any non-standard species, which in your case is the 
sheet. I recall long ago telling you this would be a challenging entity 
to parametrize, yet you quickly obtained a model and began using it. 
What verification did you perform to assure yourself that interactions 
of this ZnS sheet are reasonable in the context of protein moieties? Did 
you perform any QM interaction energies? Are there experimentally known 
binding free energies for model compounds? How do you know this model is 
appropriate?


These are all things you need to consider, and questions that are not 
within the scope of this mailing list.


-Justin


On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul  wrote:



On 2/4/18 3:25 PM, Rose wrote:


Jeah,i meant grompp :)))
and last question, i set constraint = h-Bonds, and dt=0.002 because Of
that(since usually h-Bonds have Max frequency and if i assume them
constraint so it's not reasonable to set dt=0.001 ) , is this assumption
true?


You can always decrease dt, that's "reasonable," but it makes no sense and
is inefficient. Without any form of constraints, you'd likely be limited to
dt = 0.0005 in many cases.


-Justin

Sent from my iPhone

On Feb 4, 2018, at 23:30, Justin Lemkul  wrote:



On 2/4/18 1:56 PM, Rose wrote:

Thank you so much,
Is it difference between using gmx tpbconv -extend  5ps OR use .gro
file of last simulation as an input For new 5nS
simulation?(continiuation=yes in .mdp file)


The only reason to invoke grompp is if you're changing something about
the system. For a simple continuation use tpbconv/convert-tpr and mdrun
-cpi.

-Justin

Sent from my iPhone

On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:



On 2/2/18 10:44 AM, Rose wrote:

Sent from my iPhone

On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:



On 2/2/18 8:43 AM, rose rahmani wrote:

   Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and
4nS
simulation for each window.

g_energy -f umbrella0.edr -o out.xvg

   1  Bond 2  Angle3  Proper-Dih.  4

Improper-Dih.
5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
9  Coul.-recip.10  COM-Pull-En.11  Potential   12
Kinetic-En.
   13  Total-Energy14  Conserved-En.   15  Temperature 16
Pressure

   17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20
Vir-XZ

   21  Vir-YX  22  Vir-YY  23  Vir-YZ  24
Vir-ZX

   25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28
Pres-XY

   29  Pres-XZ 30  Pres-YX 31  Pres-YY 32
Pres-YZ

   33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
#Surf*SurfTen
   37  Mu-X38  Mu-Y

   39  Mu-Z40  Coul-SR:SOL-SOL

   41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

   43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

   45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

   47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

   49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

   51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

   53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

   55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

   57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
Coul-SR:SOL-CL
   61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

   63  

Re: [gmx-users] umbrella sampling

[Nick Johans]

maybe this is irrelative but i expeienced in pulling that when i decrease
dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
crushed before(when dt=2fs)  so i had had to decrease nsteps or decrease
pull_rate , but i don't face with these crush anymore! i can pull it too
close. i know maybe these beginner confessions seem unacceptable ; and
silly.
i know this question is not accurate and can have many answers but, as a
professional and experienced person, would you please tell me, whenever you
face with  a crushed simulation, what will  you check?doubt? in your
system(separate of anything related to cpu& computers limitations) .
what cause simulations to be crushed usually?

On Mon, Feb 5, 2018 at 12:05 AM, Justin Lemkul  wrote:

>
>
> On 2/4/18 3:25 PM, Rose wrote:
>
>> Jeah,i meant grompp :)))
>> and last question, i set constraint = h-Bonds, and dt=0.002 because Of
>> that(since usually h-Bonds have Max frequency and if i assume them
>> constraint so it's not reasonable to set dt=0.001 ) , is this assumption
>> true?
>>
>
> You can always decrease dt, that's "reasonable," but it makes no sense and
> is inefficient. Without any form of constraints, you'd likely be limited to
> dt = 0.0005 in many cases.
>
>
> -Justin
>
> Sent from my iPhone
>>
>> On Feb 4, 2018, at 23:30, Justin Lemkul  wrote:
>>>
>>>
>>>
>>> On 2/4/18 1:56 PM, Rose wrote:
 Thank you so much,
 Is it difference between using gmx tpbconv -extend  5ps OR use .gro
 file of last simulation as an input For new 5nS
 simulation?(continiuation=yes in .mdp file)

>>> The only reason to invoke grompp is if you're changing something about
>>> the system. For a simple continuation use tpbconv/convert-tpr and mdrun
>>> -cpi.
>>>
>>> -Justin
>>>
>>> Sent from my iPhone

 On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:
>
>
>
> On 2/2/18 10:44 AM, Rose wrote:
>>
>> Sent from my iPhone
>>
>> On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
>>>
>>>
>>>
>>> On 2/2/18 8:43 AM, rose rahmani wrote:
   Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and
 4nS
 simulation for each window.

 g_energy -f umbrella0.edr -o out.xvg
>>
>   1  Bond 2  Angle3  Proper-Dih.  4
 Improper-Dih.
5  LJ-146  Coulomb-14   7  LJ-(SR)  8
 Coulomb-(SR)
9  Coul.-recip.10  COM-Pull-En.11  Potential   12
 Kinetic-En.
   13  Total-Energy14  Conserved-En.   15  Temperature 16
 Pressure

   17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20
 Vir-XZ

   21  Vir-YX  22  Vir-YY  23  Vir-YZ  24
 Vir-ZX

   25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28
 Pres-XY

   29  Pres-XZ 30  Pres-YX 31  Pres-YY 32
 Pres-YZ

   33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
 #Surf*SurfTen
   37  Mu-X38  Mu-Y

   39  Mu-Z40  Coul-SR:SOL-SOL

   41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

   43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

   45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

   47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

   49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

   51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

   53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

   55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

   57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
 Coul-SR:SOL-CL
   61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

   63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0

   65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0

   67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1

   69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1

   71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL

   73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL

   75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS

   77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS

   79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 2/4/18 3:25 PM, Rose wrote:

Jeah,i meant grompp :)))
and last question, i set constraint = h-Bonds, and dt=0.002 because Of  
that(since usually h-Bonds have Max frequency and if i assume them 
constraint so it's not reasonable to set dt=0.001 ) , is this assumption true?


You can always decrease dt, that's "reasonable," but it makes no sense 
and is inefficient. Without any form of constraints, you'd likely be 
limited to dt = 0.0005 in many cases.


-Justin


Sent from my iPhone


On Feb 4, 2018, at 23:30, Justin Lemkul  wrote:




On 2/4/18 1:56 PM, Rose wrote:
Thank you so much,
Is it difference between using gmx tpbconv -extend  5ps OR use .gro file of 
last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp 
file)

The only reason to invoke grompp is if you're changing something about the 
system. For a simple continuation use tpbconv/convert-tpr and mdrun -cpi.

-Justin


Sent from my iPhone


On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:




On 2/2/18 10:44 AM, Rose wrote:

Sent from my iPhone


On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:




On 2/2/18 8:43 AM, rose rahmani wrote:
  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
simulation for each window.


g_energy -f umbrella0.edr -o out.xvg

  1  Bond 2  Angle3  Proper-Dih.  4
Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
Kinetic-En.
  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure

  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ

  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX

  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY

  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ

  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
#Surf*SurfTen
  37  Mu-X38  Mu-Y

  39  Mu-Z40  Coul-SR:SOL-SOL

  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
Coul-SR:SOL-CL
  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0

  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0

  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1

  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1

  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL

  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL

  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS

  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS

  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein

  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein

  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA

  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
Coul-SR:WAL-CL
  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL

  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0

  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0

  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1

  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1

  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS

101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS

103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein

105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein

107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA

109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
Coul-SR:ZnS-CL
113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL

115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0

117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0

119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1

121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1

123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein

125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein

127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA

129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA

131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL

133  LJ-SR:Protein-CL   134  

Re: [gmx-users] umbrella sampling

[Rose]

Jeah,i meant grompp :)))
and last question, i set constraint = h-Bonds, and dt=0.002 because Of  
that(since usually h-Bonds have Max frequency and if i assume them 
constraint so it's not reasonable to set dt=0.001 ) , is this assumption true?

Sent from my iPhone

> On Feb 4, 2018, at 23:30, Justin Lemkul  wrote:
> 
> 
> 
>> On 2/4/18 1:56 PM, Rose wrote:
>> Thank you so much,
>> Is it difference between using gmx tpbconv -extend  5ps OR use .gro file of 
>> last simulation as an input For new 5nS simulation?(continiuation=yes in 
>> .mdp file)
> 
> The only reason to invoke grompp is if you're changing something about the 
> system. For a simple continuation use tpbconv/convert-tpr and mdrun -cpi.
> 
> -Justin
> 
>> 
>> Sent from my iPhone
>> 
>>> On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 2/2/18 10:44 AM, Rose wrote:
 
 Sent from my iPhone
 
> On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
> 
> 
> 
>> On 2/2/18 8:43 AM, rose rahmani wrote:
>>  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
>> simulation for each window.
>> 
 g_energy -f umbrella0.edr -o out.xvg
>>  1  Bond 2  Angle3  Proper-Dih.  4
>> Improper-Dih.
>>   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
>> Coulomb-(SR)
>>   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
>> Kinetic-En.
>>  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure
>> 
>>  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ
>> 
>>  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX
>> 
>>  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY
>> 
>>  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ
>> 
>>  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
>> #Surf*SurfTen
>>  37  Mu-X38  Mu-Y
>> 
>>  39  Mu-Z40  Coul-SR:SOL-SOL
>> 
>>  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL
>> 
>>  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL
>> 
>>  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL
>> 
>>  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS
>> 
>>  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS
>> 
>>  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein
>> 
>>  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein
>> 
>>  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA
>> 
>>  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
>> Coul-SR:SOL-CL
>>  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL
>> 
>>  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0
>> 
>>  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0
>> 
>>  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1
>> 
>>  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1
>> 
>>  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL
>> 
>>  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL
>> 
>>  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS
>> 
>>  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS
>> 
>>  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein
>> 
>>  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein
>> 
>>  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA
>> 
>>  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
>> Coul-SR:WAL-CL
>>  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL
>> 
>>  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0
>> 
>>  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0
>> 
>>  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1
>> 
>>  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1
>> 
>>  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS
>> 
>> 101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS
>> 
>> 103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein
>> 
>> 105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein
>> 
>> 107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA
>> 
>> 109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
>> Coul-SR:ZnS-CL
>> 113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL
>> 
>> 115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0
>> 
>> 117  LJ-SR:ZnS-wall0118  

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 2/4/18 1:56 PM, Rose wrote:

Thank you so much,
Is it difference between using gmx tpbconv -extend  5ps OR use .gro file of 
last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp 
file)


The only reason to invoke grompp is if you're changing something about 
the system. For a simple continuation use tpbconv/convert-tpr and mdrun 
-cpi.


-Justin



Sent from my iPhone


On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:




On 2/2/18 10:44 AM, Rose wrote:

Sent from my iPhone


On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:




On 2/2/18 8:43 AM, rose rahmani wrote:
  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
simulation for each window.


g_energy -f umbrella0.edr -o out.xvg

  1  Bond 2  Angle3  Proper-Dih.  4
Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
Kinetic-En.
  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure

  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ

  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX

  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY

  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ

  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
#Surf*SurfTen
  37  Mu-X38  Mu-Y

  39  Mu-Z40  Coul-SR:SOL-SOL

  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
Coul-SR:SOL-CL
  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0

  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0

  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1

  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1

  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL

  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL

  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS

  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS

  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein

  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein

  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA

  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
Coul-SR:WAL-CL
  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL

  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0

  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0

  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1

  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1

  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS

101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS

103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein

105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein

107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA

109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
Coul-SR:ZnS-CL
113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL

115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0

117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0

119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1

121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1

123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein

125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein

127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA

129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA

131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL

133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL

135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0

137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0

139  LJ-14:Protein-wall0140  Coul-SR:Protein-wall1

141  LJ-SR:Protein-wall1142  Coul-14:Protein-wall1

143  LJ-14:Protein-wall1144  Coul-SR:NA-NA

145  LJ-SR:NA-NA146  Coul-14:NA-NA  147  LJ-14:NA-NA148
Coul-SR:NA-CL
149  LJ-SR:NA-CL150  Coul-14:NA-CL

151  LJ-14:NA-CL152  Coul-SR:NA-wall0

153  

Re: [gmx-users] umbrella sampling

[Rose]

Thank you so much,
Is it difference between using gmx tpbconv -extend  5ps OR use .gro file of 
last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp 
file)


Sent from my iPhone

> On Feb 4, 2018, at 17:00, Justin Lemkul  wrote:
> 
> 
> 
>> On 2/2/18 10:44 AM, Rose wrote:
>> 
>> Sent from my iPhone
>> 
>>> On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 2/2/18 8:43 AM, rose rahmani wrote:
  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
 simulation for each window.
 
>> g_energy -f umbrella0.edr -o out.xvg
  1  Bond 2  Angle3  Proper-Dih.  4
 Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
 Coulomb-(SR)
   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
 Kinetic-En.
  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure
 
  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ
 
  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX
 
  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY
 
  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ
 
  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
 #Surf*SurfTen
  37  Mu-X38  Mu-Y
 
  39  Mu-Z40  Coul-SR:SOL-SOL
 
  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL
 
  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL
 
  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL
 
  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS
 
  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS
 
  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein
 
  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein
 
  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA
 
  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
 Coul-SR:SOL-CL
  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL
 
  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0
 
  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0
 
  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1
 
  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1
 
  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL
 
  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL
 
  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS
 
  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS
 
  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein
 
  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein
 
  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA
 
  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
 Coul-SR:WAL-CL
  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL
 
  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0
 
  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0
 
  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1
 
  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1
 
  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS
 
 101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS
 
 103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein
 
 105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein
 
 107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA
 
 109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
 Coul-SR:ZnS-CL
 113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL
 
 115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0
 
 117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0
 
 119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1
 
 121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1
 
 123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein
 
 125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein
 
 127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA
 
 129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA
 
 131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL
 
 133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL
 
 135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0
 
 137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0
 
 139  

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 2/2/18 10:44 AM, Rose wrote:


Sent from my iPhone


On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:




On 2/2/18 8:43 AM, rose rahmani wrote:
  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
simulation for each window.


g_energy -f umbrella0.edr -o out.xvg

  1  Bond 2  Angle3  Proper-Dih.  4
Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
Kinetic-En.
  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure

  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ

  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX

  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY

  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ

  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
#Surf*SurfTen
  37  Mu-X38  Mu-Y

  39  Mu-Z40  Coul-SR:SOL-SOL

  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
Coul-SR:SOL-CL
  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0

  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0

  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1

  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1

  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL

  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL

  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS

  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS

  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein

  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein

  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA

  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
Coul-SR:WAL-CL
  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL

  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0

  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0

  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1

  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1

  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS

101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS

103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein

105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein

107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA

109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
Coul-SR:ZnS-CL
113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL

115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0

117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0

119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1

121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1

123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein

125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein

127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA

129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA

131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL

133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL

135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0

137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0

139  LJ-14:Protein-wall0140  Coul-SR:Protein-wall1

141  LJ-SR:Protein-wall1142  Coul-14:Protein-wall1

143  LJ-14:Protein-wall1144  Coul-SR:NA-NA

145  LJ-SR:NA-NA146  Coul-14:NA-NA  147  LJ-14:NA-NA148
Coul-SR:NA-CL
149  LJ-SR:NA-CL150  Coul-14:NA-CL

151  LJ-14:NA-CL152  Coul-SR:NA-wall0

153  LJ-SR:NA-wall0 154  Coul-14:NA-wall0

155  LJ-14:NA-wall0 156  Coul-SR:NA-wall1

157  LJ-SR:NA-wall1 158  Coul-14:NA-wall1

159  LJ-14:NA-wall1 160  Coul-SR:CL-CL  161  LJ-SR:CL-CL162
Coul-14:CL-CL
163  LJ-14:CL-CL164  Coul-SR:CL-wall0

165  LJ-SR:CL-wall0 166  Coul-14:CL-wall0

167  LJ-14:CL-wall0 168  Coul-SR:CL-wall1

169  LJ-SR:CL-wall1  

Re: [gmx-users] umbrella sampling

[Nick Johans]

and i have AA between sheet and wall.and it should get closer to sheet
during pulling. How should i set the initial place of amino acid? it should
have the minimum interaction with wall and sheet , am i right?

On Fri, Feb 2, 2018 at 7:14 PM, Rose  wrote:

>
>
> Sent from my iPhone
>
> > On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
> >
> >
> >
> >> On 2/2/18 8:43 AM, rose rahmani wrote:
> >>  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
> >> simulation for each window.
> >>
>  g_energy -f umbrella0.edr -o out.xvg
> >>  1  Bond 2  Angle3  Proper-Dih.  4
> >> Improper-Dih.
> >>   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
> >> Coulomb-(SR)
> >>   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
> >> Kinetic-En.
> >>  13  Total-Energy14  Conserved-En.   15  Temperature 16
> Pressure
> >>
> >>  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ
> >>
> >>  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX
> >>
> >>  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY
> >>
> >>  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ
> >>
> >>  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
> >> #Surf*SurfTen
> >>  37  Mu-X38  Mu-Y
> >>
> >>  39  Mu-Z40  Coul-SR:SOL-SOL
> >>
> >>  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL
> >>
> >>  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL
> >>
> >>  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL
> >>
> >>  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS
> >>
> >>  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS
> >>
> >>  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein
> >>
> >>  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein
> >>
> >>  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA
> >>
> >>  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
> >> Coul-SR:SOL-CL
> >>  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL
> >>
> >>  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0
> >>
> >>  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0
> >>
> >>  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1
> >>
> >>  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1
> >>
> >>  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL
> >>
> >>  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL
> >>
> >>  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS
> >>
> >>  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS
> >>
> >>  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein
> >>
> >>  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein
> >>
> >>  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA
> >>
> >>  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
> >> Coul-SR:WAL-CL
> >>  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL
> >>
> >>  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0
> >>
> >>  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0
> >>
> >>  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1
> >>
> >>  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1
> >>
> >>  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS
> >>
> >> 101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS
> >>
> >> 103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein
> >>
> >> 105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein
> >>
> >> 107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA
> >>
> >> 109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
> >> Coul-SR:ZnS-CL
> >> 113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL
> >>
> >> 115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0
> >>
> >> 117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0
> >>
> >> 119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1
> >>
> >> 121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1
> >>
> >> 123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein
> >>
> >> 125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein
> >>
> >> 127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA
> >>
> >> 129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA
> >>
> >> 131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL
> >>
> >> 133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL
> >>
> >> 135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0
> >>
> >> 137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0
> >>
> >> 139  LJ-14:Protein-wall0140  Coul-SR:Protein-wall1
> >>
> >> 141  LJ-SR:Protein-wall1  

Re: [gmx-users] umbrella sampling

[Rose]

Sent from my iPhone

> On Feb 2, 2018, at 19:01, Justin Lemkul  wrote:
> 
> 
> 
>> On 2/2/18 8:43 AM, rose rahmani wrote:
>>  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
>> simulation for each window.
>> 
 g_energy -f umbrella0.edr -o out.xvg
>>  1  Bond 2  Angle3  Proper-Dih.  4
>> Improper-Dih.
>>   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
>> Coulomb-(SR)
>>   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
>> Kinetic-En.
>>  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure
>> 
>>  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ
>> 
>>  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX
>> 
>>  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY
>> 
>>  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ
>> 
>>  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
>> #Surf*SurfTen
>>  37  Mu-X38  Mu-Y
>> 
>>  39  Mu-Z40  Coul-SR:SOL-SOL
>> 
>>  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL
>> 
>>  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL
>> 
>>  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL
>> 
>>  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS
>> 
>>  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS
>> 
>>  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein
>> 
>>  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein
>> 
>>  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA
>> 
>>  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
>> Coul-SR:SOL-CL
>>  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL
>> 
>>  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0
>> 
>>  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0
>> 
>>  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1
>> 
>>  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1
>> 
>>  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL
>> 
>>  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL
>> 
>>  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS
>> 
>>  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS
>> 
>>  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein
>> 
>>  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein
>> 
>>  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA
>> 
>>  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
>> Coul-SR:WAL-CL
>>  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL
>> 
>>  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0
>> 
>>  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0
>> 
>>  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1
>> 
>>  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1
>> 
>>  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS
>> 
>> 101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS
>> 
>> 103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein
>> 
>> 105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein
>> 
>> 107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA
>> 
>> 109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
>> Coul-SR:ZnS-CL
>> 113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL
>> 
>> 115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0
>> 
>> 117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0
>> 
>> 119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1
>> 
>> 121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1
>> 
>> 123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein
>> 
>> 125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein
>> 
>> 127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA
>> 
>> 129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA
>> 
>> 131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL
>> 
>> 133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL
>> 
>> 135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0
>> 
>> 137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0
>> 
>> 139  LJ-14:Protein-wall0140  Coul-SR:Protein-wall1
>> 
>> 141  LJ-SR:Protein-wall1142  Coul-14:Protein-wall1
>> 
>> 143  LJ-14:Protein-wall1144  Coul-SR:NA-NA
>> 
>> 145  LJ-SR:NA-NA146  Coul-14:NA-NA  147  LJ-14:NA-NA148
>> Coul-SR:NA-CL
>> 149  LJ-SR:NA-CL150  Coul-14:NA-CL
>> 
>> 151  LJ-14:NA-CL152  Coul-SR:NA-wall0
>> 
>> 153  LJ-SR:NA-wall0 154  Coul-14:NA-wall0
>> 
>> 155  LJ-14:NA-wall0 156  Coul-SR:NA-wall1
>> 
>> 157  

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 2/2/18 8:43 AM, rose rahmani wrote:

  Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
simulation for each window.


g_energy -f umbrella0.edr -o out.xvg

  1  Bond 2  Angle3  Proper-Dih.  4
Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
   9  Coul.-recip.10  COM-Pull-En.11  Potential   12
Kinetic-En.
  13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure

  17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ

  21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX

  25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY

  29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ

  33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
#Surf*SurfTen
  37  Mu-X38  Mu-Y

  39  Mu-Z40  Coul-SR:SOL-SOL

  41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

  43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

  45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

  47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

  49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

  51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

  53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

  55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

  57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
Coul-SR:SOL-CL
  61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

  63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0

  65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0

  67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1

  69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1

  71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL

  73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL

  75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS

  77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS

  79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein

  81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein

  83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA

  85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
Coul-SR:WAL-CL
  89  LJ-SR:WAL-CL90  Coul-14:WAL-CL

  91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0

  93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0

  95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1

  97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1

  99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS

101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS

103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein

105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein

107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA

109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
Coul-SR:ZnS-CL
113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL

115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0

117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0

119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1

121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1

123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein

125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein

127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA

129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA

131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL

133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL

135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0

137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0

139  LJ-14:Protein-wall0140  Coul-SR:Protein-wall1

141  LJ-SR:Protein-wall1142  Coul-14:Protein-wall1

143  LJ-14:Protein-wall1144  Coul-SR:NA-NA

145  LJ-SR:NA-NA146  Coul-14:NA-NA  147  LJ-14:NA-NA148
Coul-SR:NA-CL
149  LJ-SR:NA-CL150  Coul-14:NA-CL

151  LJ-14:NA-CL152  Coul-SR:NA-wall0

153  LJ-SR:NA-wall0 154  Coul-14:NA-wall0

155  LJ-14:NA-wall0 156  Coul-SR:NA-wall1

157  LJ-SR:NA-wall1 158  Coul-14:NA-wall1

159  LJ-14:NA-wall1 160  Coul-SR:CL-CL  161  LJ-SR:CL-CL162
Coul-14:CL-CL
163  LJ-14:CL-CL164  Coul-SR:CL-wall0

165  LJ-SR:CL-wall0 166  Coul-14:CL-wall0

167  LJ-14:CL-wall0 168  Coul-SR:CL-wall1

169  LJ-SR:CL-wall1 170  Coul-14:CL-wall1

171  LJ-14:CL-wall1 172  Coul-SR:wall0-wall0

173  

Re: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

[金 瑞涛]

Hello

Have you tried different pressure coupling type? Maybe a semi-isotropic one 
will solve the problem if you chose z-axis as your pulling vector direction.

Best regards

Riotto



Sent from my Samsung Galaxy smartphone.


 Original message 
From: Shrinath Kumar 
Date: 28/1/18 12:53 am (GMT+10:00)
To: gmx-us...@gromacs.org
Subject: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 
times box size error

Hi,

I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big nor can
I use pull-geometry = direction-periodic as I need to use NPT.

But I'm confused on why I get this error in the first place because my
periodic box is a cuboid and the pulling distance is less than 0.5*box size
in each dimension. So the pulling vector should be uniquely determined and
there should be no discontinuities.

To solve this I tried having 3 pull coordinates each acting on a separate
dimension. This solves the grompp error. But would this produce the same
results as having 1 pull coordinate acting on all 3 dimensions? Or is there
any better workaround for this?

Thanks,
Shrinath
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 1/18/18 12:37 AM, Moradzadeh, Alireza wrote:

Hi!

I am trying to do umbrella sampling between two 2D-sheets. I did it according 
bevan lab tutorial the problem I encounter is that after pulling steps. I 
perform umbrella sampling with rate of 0.0  however, two sheets get back 
together and initial configuration and final configuration are totally 
different. Z_start = 0.91 nm and Z_Final = 0.51 nm. Any possible solution?


Use a stronger force constant.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Umbrella sampling-gmx distance

[rose rahmani]

Oops,Sorrry. Sometimes big challenges make ones think hard and ignore
obvious issues.
Thank you so much Mr.justin and joao

On Sat, Jan 13, 2018 at 4:01 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> The output is very explicitly telling you what the problem is. You didn't
> provide a topology. Pass one the the -s flag.  How do you want the COM to
> be computed when you're not providing any masses?
>
> J
>
> On Jan 13, 2018 9:19 AM, "rose rahmani"  wrote:
>
> > I'm relly sorry for asking you again and again but...
> >
> > GROMACS:  gmx distance, VERSION 5.1.4
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
> > of group 6'
> >
> >
> > ---
> > Program: gmx distance, VERSION 5.1.4
> > Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
> > Function:void
> > gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::
> > SelectionCollection*)
> >
> > Inconsistency in user input:
> > No topology provided, but one is required for analysis
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > Whai is the problem?;(
> >
> > On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 1/11/18 11:38 AM, rose rahmani wrote:
> > >
> > >>   [ ZnS ]
> > >> 123456789   10   11   12   13   14
> > >>  15
> > >>16   17   18   19   20   21   22   23   24   25   26   27   28   29
> > >>  30
> > >>31   32   33   34   35   36   37   38   39   40   41   42   43   44
> > >>   45..
> > >>
> > >> [ Protein ]
> > >>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
> > >> 775
> > >>   776  777  778  779  780  781  782  783  784  785  786
> > >>
> > >> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
> > >> "ZnS"
> > >> plus com of group "Protein"' -oxyz -oall
> > >> i exactly select index groups!!!
> > >> ---
> > >> Program: gmx distance, VERSION 5.1.4
> > >> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
> > >> Function:void gmx::SelectionCollection::setI
> > >> ndexGroups(gmx_ana_indexgrps_t*)
> > >>
> > >> Inconsistency in user input:
> > >> Invalid index group reference(s)
> > >>Cannot match 'group "ZnS"', because no such index group can be
> found.
> > >>Cannot match 'group "Protein"', because no such index group can be
> > >> found.
> > >>
> > >> For more information and tips for troubleshooting, please check the
> > >> GROMACS
> > >> website at http://www.gromacs.org/Documentation/Errors
> > >> 
> > >> -
> > >> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
> > >> -select -oxyz
> > >> GROMACS:  gmx distance, VERSION 5.1.4
> > >> Executable:   /usr/local/gromacs/bin/gmx
> > >> Data prefix:  /usr/local/gromacs
> > >> Command line:
> > >>gmx distance -n index.ndx -f conf0.gro -select -oxyz
> > >>
> > >> Available static index groups:
> > >>   Group  0 "System" (4336 atoms)
> > >>   Group  1 "Other" (760 atoms)
> > >>   Group  2 "ZnS" (560 atoms)
> > >>   Group  3 "WAL" (200 atoms)
> > >>   Group  4 "NA" (5 atoms)
> > >>   Group  5 "CL" (5 atoms)
> > >>   Group  6 "Protein" (26 atoms)
> > >>   Group  7 "Protein-H" (12 atoms)
> > >> .
> > >> .
> > >> (one per line,  for status/groups, 'help' for help, Ctrl-D to
> > end)
> > >>
> > >>> 2
> > >>>
> > >> Selection '2' parsed
> > >>
> > >>> 6
> > >>>
> > >> Selection '6' parsed
> > >>
> > >
> > > You should be selecting 'com of group 2' etc. here to get what you
> want.
> > I
> > > don't know why the command-line version of this didn't work, but to
> get a
> > > COM distance, you need to tell gmx distance to do it, otherwise it's
> just
> > > going to produce pairwise distances, which is what you're asking for
> > here.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe 

Re: [gmx-users] Umbrella sampling-gmx distance

[João Henriques]

The output is very explicitly telling you what the problem is. You didn't
provide a topology. Pass one the the -s flag.  How do you want the COM to
be computed when you're not providing any masses?

J

On Jan 13, 2018 9:19 AM, "rose rahmani"  wrote:

> I'm relly sorry for asking you again and again but...
>
> GROMACS:  gmx distance, VERSION 5.1.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
> of group 6'
>
>
> ---
> Program: gmx distance, VERSION 5.1.4
> Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
> Function:void
> gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::
> SelectionCollection*)
>
> Inconsistency in user input:
> No topology provided, but one is required for analysis
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> Whai is the problem?;(
>
> On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 1/11/18 11:38 AM, rose rahmani wrote:
> >
> >>   [ ZnS ]
> >> 123456789   10   11   12   13   14
> >>  15
> >>16   17   18   19   20   21   22   23   24   25   26   27   28   29
> >>  30
> >>31   32   33   34   35   36   37   38   39   40   41   42   43   44
> >>   45..
> >>
> >> [ Protein ]
> >>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
> >> 775
> >>   776  777  778  779  780  781  782  783  784  785  786
> >>
> >> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
> >> "ZnS"
> >> plus com of group "Protein"' -oxyz -oall
> >> i exactly select index groups!!!
> >> ---
> >> Program: gmx distance, VERSION 5.1.4
> >> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
> >> Function:void gmx::SelectionCollection::setI
> >> ndexGroups(gmx_ana_indexgrps_t*)
> >>
> >> Inconsistency in user input:
> >> Invalid index group reference(s)
> >>Cannot match 'group "ZnS"', because no such index group can be found.
> >>Cannot match 'group "Protein"', because no such index group can be
> >> found.
> >>
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >> 
> >> -
> >> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
> >> -select -oxyz
> >> GROMACS:  gmx distance, VERSION 5.1.4
> >> Executable:   /usr/local/gromacs/bin/gmx
> >> Data prefix:  /usr/local/gromacs
> >> Command line:
> >>gmx distance -n index.ndx -f conf0.gro -select -oxyz
> >>
> >> Available static index groups:
> >>   Group  0 "System" (4336 atoms)
> >>   Group  1 "Other" (760 atoms)
> >>   Group  2 "ZnS" (560 atoms)
> >>   Group  3 "WAL" (200 atoms)
> >>   Group  4 "NA" (5 atoms)
> >>   Group  5 "CL" (5 atoms)
> >>   Group  6 "Protein" (26 atoms)
> >>   Group  7 "Protein-H" (12 atoms)
> >> .
> >> .
> >> (one per line,  for status/groups, 'help' for help, Ctrl-D to
> end)
> >>
> >>> 2
> >>>
> >> Selection '2' parsed
> >>
> >>> 6
> >>>
> >> Selection '6' parsed
> >>
> >
> > You should be selecting 'com of group 2' etc. here to get what you want.
> I
> > don't know why the command-line version of this didn't work, but to get a
> > COM distance, you need to tell gmx distance to do it, otherwise it's just
> > going to produce pairwise distances, which is what you're asking for
> here.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to 

Re: [gmx-users] Umbrella sampling-gmx distance

[rose rahmani]

I'm relly sorry for asking you again and again but...

GROMACS:  gmx distance, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
of group 6'


---
Program: gmx distance, VERSION 5.1.4
Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
Function:void
gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::SelectionCollection*)

Inconsistency in user input:
No topology provided, but one is required for analysis

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Whai is the problem?;(

On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul  wrote:

>
>
> On 1/11/18 11:38 AM, rose rahmani wrote:
>
>>   [ ZnS ]
>> 123456789   10   11   12   13   14
>>  15
>>16   17   18   19   20   21   22   23   24   25   26   27   28   29
>>  30
>>31   32   33   34   35   36   37   38   39   40   41   42   43   44
>>   45..
>>
>> [ Protein ]
>>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
>> 775
>>   776  777  778  779  780  781  782  783  784  785  786
>>
>> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
>> "ZnS"
>> plus com of group "Protein"' -oxyz -oall
>> i exactly select index groups!!!
>> ---
>> Program: gmx distance, VERSION 5.1.4
>> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
>> Function:void gmx::SelectionCollection::setI
>> ndexGroups(gmx_ana_indexgrps_t*)
>>
>> Inconsistency in user input:
>> Invalid index group reference(s)
>>Cannot match 'group "ZnS"', because no such index group can be found.
>>Cannot match 'group "Protein"', because no such index group can be
>> found.
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> -
>> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
>> -select -oxyz
>> GROMACS:  gmx distance, VERSION 5.1.4
>> Executable:   /usr/local/gromacs/bin/gmx
>> Data prefix:  /usr/local/gromacs
>> Command line:
>>gmx distance -n index.ndx -f conf0.gro -select -oxyz
>>
>> Available static index groups:
>>   Group  0 "System" (4336 atoms)
>>   Group  1 "Other" (760 atoms)
>>   Group  2 "ZnS" (560 atoms)
>>   Group  3 "WAL" (200 atoms)
>>   Group  4 "NA" (5 atoms)
>>   Group  5 "CL" (5 atoms)
>>   Group  6 "Protein" (26 atoms)
>>   Group  7 "Protein-H" (12 atoms)
>> .
>> .
>> (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
>>
>>> 2
>>>
>> Selection '2' parsed
>>
>>> 6
>>>
>> Selection '6' parsed
>>
>
> You should be selecting 'com of group 2' etc. here to get what you want. I
> don't know why the command-line version of this didn't work, but to get a
> COM distance, you need to tell gmx distance to do it, otherwise it's just
> going to produce pairwise distances, which is what you're asking for here.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

[Justin Lemkul]

On 1/12/18 7:09 AM, rose rahmani wrote:

I had this problem but i couldn't solve it.
  But i can tell you just a temporary solution; Don't use -sep with
trjconv,then use the output conf as an input for gmx distance. it probably
gives you sth like this;

time   distances
0.0001.75372870.02386010.0428935   -1.7530417
2.0001.7294775   -0.0426260   -0.0664551   -1.7276745
4.0001.71536770.06641650.0698769   -1.7126565
   .
.
.
.
just consider that time=2 >>> is 1 ps ( depends on dt )
   =4  >>> is  2ps
   = 6  >>> is  3ps .
but distances are exactly the same.
Sorrry, i know maybe Dr.justin and all professionals don't agree with these
solutions, but i can understand,when you don't get a proper answer,
sometimes you have to ridiculous solutions.That's it!


It's not ridiculous, but there is logic in either approach. My preferred 
approach is to use trjconv -sep to quickly extract every frame, compile 
the distances of each with consistent labels (frame numbers, not time) 
and then you very easily (1) have the coordinate files already extracted 
and (2) you know exactly which frames to use by frame number.


Without using my approach, one can easily analyze the entire trajectory 
(perfectly fine) but then manually go back using trjconv -dump and 
specify the desired frames by time. I find this to be tedious and not 
easily automated.


-Justin



On Fri, Jan 12, 2018 at 10:44 AM, "Ashwini Londhe" <615...@kist.re.kr>
wrote:




Hi


Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very
fine. so I following the same tutorial for ligand-protein complex.


I have pulled the ligand over 300ps using following MD_pull.mdp and also
generated  series of cordinate files (conf0.gro-conf300.gro) but problem is
at distance calculation.





title = Umbrella pulling simulation


define = -DPOSRES

; Run parameters

integrator = md

dt = 0.002

tinit = 0

nsteps = 15 ; 300 ps


nstcomm = 10

; Output parameters

nstxout = 5000 ; every 10 ps

nstvout = 5000

nstfout = 500

nstxtcout = 500 ; every 1 ps

nstenergy = 500

; Bond parameters

constraint_algorithm = lincs


constraints = all-bonds

continuation = yes ; continuing from NPT

; Single-range cutoff scheme

nstlist = 5

ns_type = grid

rlist = 1.4

rcoulomb = 1.4

rvdw = 1.4

; PME electrostatics parameters

coulombtype = PME

fourierspacing = 0.12

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes


; Berendsen temperature coupling is on in two groups

Tcoupl = Nose-Hoover

tc_grps = Protein Non-Protein

tau_t = 0.5 0.5

ref_t = 310 310

; Pressure coupling is on

Pcoupl = Parrinello-Rahman

pcoupltype = isotropic

tau_p = 1.0

compressibility = 4.5e-5

ref_p = 1.0

refcoord_scaling = com

; Generate velocities is off

gen_vel = no

; Periodic boundary conditions are on in all directions

pbc = xyz

; Long-range dispersion correction

DispCorr = EnerPres

; Pull code

pull = yes

pull_ngroups = 2

pull_ncoords = 1


pull_group1_name = Protein


pull_group2_name = L6I


pull_coord1_type = umbrella ; harmonic biasing force


pull_coord1_geometry = distance ; simple distance increase


pull_coord1_groups = 1 2


pull_coord1_dim = N N Y


pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns


pull_coord1_k = 1000 ; kJ mol^-1 nm^-2


pull_coord1_start = yes ; define initial COM distance > 0





I have used distances.pl file from gromacs tutorial and change the group
name Chain_A and Chain_B with L6I and Protein. Also replaced 500 frames
with 300 frames. It generated summary_distance.dat file which does not
include distances values.


  After running script it generates this at the end


.


.


.


Processing configuration 300...


readline () on closed filehandle IN at distances.pl line 16.


Use of uninitializd value $distance in concatenaton (.) or string at
distans.pl line 30





How could it happen by just changing Chain_A to L6I and Chain_B to Protein
and conformations 500 to 300 it seems script works fine for peptide system
only and not for protein_ligand complex.





Also above error generated for ony proein-ligand complex and not for the
peptide tutoral.


Please help me to sort out this problem.





Regards


Ashwini Londhe



Korea Institute of Science and Technology (KIST)
5, Hwarang-ro 14-gil
Seongbuk-gu
Seoul, 02792
Republic of Korea


(우: 02792) 서울특별시 성북구 화랑로 14길 5
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia 

Re: [gmx-users] Umbrella sampling-gmx distance

[Justin Lemkul]

On 1/11/18 11:38 AM, rose rahmani wrote:

  [ ZnS ]
123456789   10   11   12   13   14   15
   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
   31   32   33   34   35   36   37   38   39   40   41   42   43   44
  45..

[ Protein ]
  761  762  763  764  765  766  767  768  769  770  771  772  773  774  775
  776  777  778  779  780  781  782  783  784  785  786

command; gmx distance -n index.ndx -f conf0.gro -select 'com of group "ZnS"
plus com of group "Protein"' -oxyz -oall
i exactly select index groups!!!
---
Program: gmx distance, VERSION 5.1.4
Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
Function:void gmx::SelectionCollection::setI
ndexGroups(gmx_ana_indexgrps_t*)

Inconsistency in user input:
Invalid index group reference(s)
   Cannot match 'group "ZnS"', because no such index group can be found.
   Cannot match 'group "Protein"', because no such index group can be found.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

-
so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
-select -oxyz
GROMACS:  gmx distance, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
   gmx distance -n index.ndx -f conf0.gro -select -oxyz

Available static index groups:
  Group  0 "System" (4336 atoms)
  Group  1 "Other" (760 atoms)
  Group  2 "ZnS" (560 atoms)
  Group  3 "WAL" (200 atoms)
  Group  4 "NA" (5 atoms)
  Group  5 "CL" (5 atoms)
  Group  6 "Protein" (26 atoms)
  Group  7 "Protein-H" (12 atoms)
.
.
(one per line,  for status/groups, 'help' for help, Ctrl-D to end)

2

Selection '2' parsed

6

Selection '6' parsed


You should be selecting 'com of group 2' etc. here to get what you want. 
I don't know why the command-line version of this didn't work, but to 
get a COM distance, you need to tell gmx distance to do it, otherwise 
it's just going to produce pairwise distances, which is what you're 
asking for here.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

[rose rahmani]

I had this problem but i couldn't solve it.
 But i can tell you just a temporary solution; Don't use -sep with
trjconv,then use the output conf as an input for gmx distance. it probably
gives you sth like this;

time   distances
   0.0001.75372870.02386010.0428935   -1.7530417
   2.0001.7294775   -0.0426260   -0.0664551   -1.7276745
   4.0001.71536770.06641650.0698769   -1.7126565
  .
.
.
.
just consider that time=2 >>> is 1 ps ( depends on dt )
  =4  >>> is  2ps
  = 6  >>> is  3ps .
but distances are exactly the same.
Sorrry, i know maybe Dr.justin and all professionals don't agree with these
solutions, but i can understand,when you don't get a proper answer,
sometimes you have to ridiculous solutions.That's it!


On Fri, Jan 12, 2018 at 10:44 AM, "Ashwini Londhe" <615...@kist.re.kr>
wrote:

>
>
>
> Hi
>
>
> Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very
> fine. so I following the same tutorial for ligand-protein complex.
>
>
> I have pulled the ligand over 300ps using following MD_pull.mdp and also
> generated  series of cordinate files (conf0.gro-conf300.gro) but problem is
> at distance calculation.
>
>
>
>
>
> title = Umbrella pulling simulation
>
>
> define = -DPOSRES
>
> ; Run parameters
>
> integrator = md
>
> dt = 0.002
>
> tinit = 0
>
> nsteps = 15 ; 300 ps
>
>
> nstcomm = 10
>
> ; Output parameters
>
> nstxout = 5000 ; every 10 ps
>
> nstvout = 5000
>
> nstfout = 500
>
> nstxtcout = 500 ; every 1 ps
>
> nstenergy = 500
>
> ; Bond parameters
>
> constraint_algorithm = lincs
>
>
> constraints = all-bonds
>
> continuation = yes ; continuing from NPT
>
> ; Single-range cutoff scheme
>
> nstlist = 5
>
> ns_type = grid
>
> rlist = 1.4
>
> rcoulomb = 1.4
>
> rvdw = 1.4
>
> ; PME electrostatics parameters
>
> coulombtype = PME
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = Nose-Hoover
>
> tc_grps = Protein Non-Protein
>
> tau_t = 0.5 0.5
>
> ref_t = 310 310
>
> ; Pressure coupling is on
>
> Pcoupl = Parrinello-Rahman
>
> pcoupltype = isotropic
>
> tau_p = 1.0
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> refcoord_scaling = com
>
> ; Generate velocities is off
>
> gen_vel = no
>
> ; Periodic boundary conditions are on in all directions
>
> pbc = xyz
>
> ; Long-range dispersion correction
>
> DispCorr = EnerPres
>
> ; Pull code
>
> pull = yes
>
> pull_ngroups = 2
>
> pull_ncoords = 1
>
>
> pull_group1_name = Protein
>
>
> pull_group2_name = L6I
>
>
> pull_coord1_type = umbrella ; harmonic biasing force
>
>
> pull_coord1_geometry = distance ; simple distance increase
>
>
> pull_coord1_groups = 1 2
>
>
> pull_coord1_dim = N N Y
>
>
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>
>
> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
>
>
> pull_coord1_start = yes ; define initial COM distance > 0
>
>
>
>
>
> I have used distances.pl file from gromacs tutorial and change the group
> name Chain_A and Chain_B with L6I and Protein. Also replaced 500 frames
> with 300 frames. It generated summary_distance.dat file which does not
> include distances values.
>
>
>  After running script it generates this at the end
>
>
> .
>
>
> .
>
>
> .
>
>
> Processing configuration 300...
>
>
> readline () on closed filehandle IN at distances.pl line 16.
>
>
> Use of uninitializd value $distance in concatenaton (.) or string at
> distans.pl line 30
>
>
>
>
>
> How could it happen by just changing Chain_A to L6I and Chain_B to Protein
> and conformations 500 to 300 it seems script works fine for peptide system
> only and not for protein_ligand complex.
>
>
>
>
>
> Also above error generated for ony proein-ligand complex and not for the
> peptide tutoral.
>
>
> Please help me to sort out this problem.
>
>
>
>
>
> Regards
>
>
> Ashwini Londhe
>
>
>
> Korea Institute of Science and Technology (KIST)
> 5, Hwarang-ro 14-gil
> Seongbuk-gu
> Seoul, 02792
> Republic of Korea
>
>
> (우: 02792) 서울특별시 성북구 화랑로 14길 5
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Umbrella Sampling-gmx distance

[Justin Lemkul]

On 1/11/18 9:50 AM, rose rahmani wrote:

still like this


You're not using the command syntax shown in the link I provided.

-Justin


# This file was created Thu Jan 11 09:46:46 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable:   /usr/local/gromacs/bin/gmx
# Data prefix:  /usr/local/gromacs
# Command line:
#   gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg
# gmx distance is part of G R O M A C S:
#
#
¸<8d><9e><89><9a><93>í<8a><9d><8c>ð<99><8b><9a><91>ò<9e><91><86>þ<88><99><8a><93><93><86>ü<9e><8a><8b><9a><8d><96><85><9ì<90><8d><9a><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
   0.0000.1920.2700.191   -0.192   -0.2700.1910.383
   0.0000.0000.3830.0000.0000.3830.0000.000
0.3830.0000.0001.1310.2700.1910.3820.000
0.0000.3820.0000.0000.3830.0000.0000.383
0.0000.0000.3830.0000.0000.3830.0000.000
0.3830.0000.0000.3820.0000.0000.748   -0.270
0.1910.3820.0000.0000.3820.0000.0000.382
0.0000.0000.3820.0000.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.1920.2700.191
  -0.192   -0.2700.1910.3830.0000.0000.3830.000
0.0000.3830.0000.0000.3830.0000.0001.131
0.2700.1910.3820.0000.0000.3820.0000.000
0.3830.0000.0000.3830.0000.0000.3830.000
0.0000.3830.0000.0000.3830.0000.0000.382
0.0000.0000.748   -0.2700.1910.3820.0000.000
0.3820.0000.0000.3820.0000.0000.3820.000
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.541

Re: [gmx-users] Umbrella Sampling-gmx distance

[rose rahmani]

still like this

# This file was created Thu Jan 11 09:46:46 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable:   /usr/local/gromacs/bin/gmx
# Data prefix:  /usr/local/gromacs
# Command line:
#   gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg
# gmx distance is part of G R O M A C S:
#
#
¸<8d><9e><89><9a><93>í<8a><9d><8c>ð<99><8b><9a><91>ò<9e><91><86>þ<88><99><8a><93><93><86>ü<9e><8a><8b><9a><8d><96><85><9ì<90><8d><9a><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
  0.0000.1920.2700.191   -0.192   -0.2700.1910.383
  0.0000.0000.3830.0000.0000.3830.0000.000
0.3830.0000.0001.1310.2700.1910.3820.000
0.0000.3820.0000.0000.3830.0000.0000.383
0.0000.0000.3830.0000.0000.3830.0000.000
0.3830.0000.0000.3820.0000.0000.748   -0.270
0.1910.3820.0000.0000.3820.0000.0000.382
0.0000.0000.3820.0000.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.1920.2700.191
 -0.192   -0.2700.1910.3830.0000.0000.3830.000
0.0000.3830.0000.0000.3830.0000.0001.131
0.2700.1910.3820.0000.0000.3820.0000.000
0.3830.0000.0000.3830.0000.0000.3830.000
0.0000.3830.0000.0000.3830.0000.0000.382
0.0000.0000.748   -0.2700.1910.3820.0000.000
0.3820.0000.0000.3820.0000.0000.3820.000
0.0000.0000.5410.0000.0000.5410.0000.000
0.5410.0000.0000.5410.0000.0000.5410.000
0.0000.5410.0000.0000.5410.0000.0000.541
0.0000.0000.5410.0000.000

Re: [gmx-users] Umbrella Sampling-gmx distance

[Justin Lemkul]

On 1/11/18 3:43 AM, rose rahmani wrote:

Hi

i'm doing umbella sampling. whenever i use gmx distance after pulling in
V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp
file for pulling:

integrator   = md
dt   = 0.001
nsteps   = 250
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
cutoff_scheme= group
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= direction
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate= -0.001
pull_coord1_k   = 5000
pull_coord1_start   = yes
pull_nstxout= 10


and this is dist0.xvg

# This file was created Thu Jan 11 03:19:07 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable:   /usr/local/gromacs/bin/gmx
# Data prefix:  /usr/local/gromacs
# Command line:
#   gmx distance -s pull.tpr -n index.ndx -f conf0.gro -oall dist0.xvg


By using -oall, you're getting a matrix of all distances between the 
atoms in the selected groups. You just want a COM distance, so you need 
-oxyz with a suitable COM selection (see 
http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-dist)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] umbrella sampling, LINCS WARNING

[Justin Lemkul]

On 1/4/18 2:48 AM, rose rahmani wrote:

Hello;

I'm doing umbrella sampling, protein is getting closer to ZnS, but i get
some step files and run crashed just 107sec to end. Would it be because of
protein got very close to ZnS? Would you please help me?


A COM distance of 0.3 nm is going to place atoms well within the steep 
LJ repulsive regime, so naturally forces are going to build up. Watch 
the trajectory and see what's happening.


-Justin


With regards


-
this is pullf.xvg

0.  -0.000579208
0.0020  2.45011
0.0040  4.89696
0.0060  7.35804
0.0080  9.82449
0.0100  12.2863
0.0120  14.7352
0.0140  17.1628
0.0160  19.5634

.
.
.
1956.0480   -100532
1956.0500   -100532
1956.0520   -100531
1956.0540   -100530
1956.0560   -100529
1956.0580   -100528
1956.0600   -100527
1956.0620   -100526
---
this is pullx.xvg

0.  4.287   1.73577
0.1000  4.287   1.72023
0.2000  4.287   1.73131
0.3000  4.287   1.75326
0.4000  4.287   1.77348
0.5000  4.287   1.76939
0.6000  4.287   1.75636
0.7000  4.287   1.73677
0.8000  4.287   1.71755
0.9000  4.287   1.70901
1.  4.287   1.72336

.
.
.

1953.2000   4.287   0.324765
1953.3000   4.287   0.323972
1953.4000   4.287   0.326929
1953.5000   4.287   0.323881
1953.6000   4.287   0.323358
1953.7000   4.287   0.325145
1953.8000   4.287   0.32516
1953.9000   4.287   0.324791
1954.   4.287   0.325144
1954.1000   4.287   0.324902
1954.2000   4.287   0.324985
1954.3000   4.287   0.324877
1954.4000   4.287   0.323429
1954.5000   4.287   0.32637
1954.6000   4.287   0.324941
1954.7000   4.

---
this is md_pull.mdp;

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = -0.011; 1 nm per  ns
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50

--
This is pull.job


Step 978195, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.04, max 0.10 (between atoms 782 and 780)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 770769   61.40.1090   0.1090  0.1090
 779778   42.00.1010   0.1010  0.1010

Step 978197, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.429802, max 1.468930 (between atoms 783 and 780)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 773771   90.00.1112   0.1202  0.1090
 770769   32.80.1090   0.1090  0.1090
 779778   90.00.1010   0.1232  0.1010
 783780   90.00.1090   0.2691  0.1090
Wrote pdb files with previous and current coordinates

Step 978198, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212948, max 5.521000 (between atoms 773 and 771)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 773771   90.00.1202   0.7108  0.1090
 772771   47.80.1105   0.1031  0.1090
 770769   90.00.1090   0.1142  0.1090
 779778   90.00.1232   0.6381  0.1010
 783780   57.80.2691   0.1086  0.1090
Wrote pdb files with previous and current coordinates

Step 978199, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.451943, max 1.210712 (between atoms 770 and 769)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  

Re: [gmx-users] Umbrella sampling

[Jefferies D . F .]

All sorted now. 

Thanks, 

Damien 

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Friday, December 22, 2017 11:49 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

  - Message from Mark Abraham <mark.j.abra...@gmail.com> -
Date: Fri, 22 Dec 2017 00:42:31 +
From: Mark Abraham <mark.j.abra...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
  To: gmx-us...@gromacs.org
  Cc: gromacs.org_gmx-users@maillist.sys.kth.se

> Hi,
>
> Yes, the parsing of that file looks like it doesn't handle blank lines
> gracefully, at least. Use a text editor and clean things up. And make
sure
> the file endings are unix style, e.g. with dos2unix if relevant.
>
> Mark
>
> On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. <dfj1...@soton.ac.uk>
> wrote:
>
>> Out of curiosity, how did you manage to identify and subsequently remove
>> the extra space? I have been having similar problems and the tools I've
>> used haven't fixed this problem.
>>
>> Thanks,
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
>> sp...@iacs.res.in [sp...@iacs.res.in]
>> Sent: Tuesday, December 19, 2017 6:21 PM
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Umbrella sampling
>>
>>   - Message from Dhaniram Mahato <bioinfo...@gmail.com> -
>>     Date: Tue, 19 Dec 2017 21:30:05 +0800
>> From: Dhaniram Mahato <bioinfo...@gmail.com>
>> Reply-To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Umbrella sampling
>>   To: gmx-us...@gromacs.org
>>
>> Hi,
>>
>> There could be format problem. You can create your own .dat files by
>> typing
>> it. You have probably copied it from somewhere. I hope it will work
then.
>>
>>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>>
>> Thanks
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-requ...@gromacs.org.
>>
>> Hii
>> I have solved the problem. It was just because of one extra space added
>> in
>> the tpr-files.dat file. Now its running properly.
>>
>> - End message from Dhaniram Mahato <bioinfo...@gmail.com> -
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
>> * For (un)subscribe requests visit
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>> send a mail to gmx-users-requ...@gromacs.org.
>
> --
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> * Please search the archive at
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> posting!
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Thank you Mark for your suggestion.

- End message from Mark Abraham <mark.j.abra...@gmail.com> -
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Re: [gmx-users] Umbrella sampling

[spss4]

 - Message from Mark Abraham <mark.j.abra...@gmail.com> -
    Date: Fri, 22 Dec 2017 00:42:31 +
    From: Mark Abraham <mark.j.abra...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-us...@gromacs.org
      Cc: gromacs.org_gmx-users@maillist.sys.kth.se


Hi,

Yes, the parsing of that file looks like it doesn't handle blank lines
gracefully, at least. Use a text editor and clean things up. And make

sure

the file endings are unix style, e.g. with dos2unix if relevant.

Mark

On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. <dfj1...@soton.ac.uk>
wrote:


Out of curiosity, how did you manage to identify and subsequently remove
the extra space? I have been having similar problems and the tools I've
used haven't fixed this problem.

Thanks,

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Tuesday, December 19, 2017 6:21 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

  - Message from Dhaniram Mahato <bioinfo...@gmail.com> -
    Date: Tue, 19 Dec 2017 21:30:05 +0800
    From: Dhaniram Mahato <bioinfo...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-us...@gromacs.org

Hi,

There could be format problem. You can create your own .dat files by
typing
it. You have probably copied it from somewhere. I hope it will work

then.




https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html


Thanks
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Hii
I have solved the problem. It was just because of one extra space added
in
the tpr-files.dat file. Now its running properly.

- End message from Dhaniram Mahato <bioinfo...@gmail.com> -
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Thank you Mark for your suggestion.

- End message from Mark Abraham <mark.j.abra...@gmail.com> -
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Re: [gmx-users] Umbrella sampling

[spss4]

 - Message from "Jefferies D.F." <dfj1...@soton.ac.uk> -
    Date: Tue, 19 Dec 2017 20:56:34 +
    From: "Jefferies D.F." <dfj1...@soton.ac.uk>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-us...@gromacs.org,
gromacs.org_gmx-users@maillist.sys.kth.se


Out of curiosity, how did you manage to identify and subsequently remove
the extra space? I have been having similar problems and the tools I've
used haven't fixed this problem.

Thanks,

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Tuesday, December 19, 2017 6:21 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

- Message from Dhaniram Mahato <bioinfo...@gmail.com> -
   Date: Tue, 19 Dec 2017 21:30:05 +0800
   From: Dhaniram Mahato <bioinfo...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
     To: gmx-us...@gromacs.org


Hi,

There could be format problem. You can create your own .dat files by
typing
it. You have probably copied it from somewhere. I hope it will work

then.

 




https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html

Thanks
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Hii
I have solved the problem. It was just because of one extra space added

in

the tpr-files.dat file. Now its running properly.

- End message from Dhaniram Mahato <bioinfo...@gmail.com> -
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Hii
In my tpr-files.dat file as I showed in the first mail, one extra blank
line was added at the bottom of the file. I just deleted that line and the
problem has been solved. You just open your .dat file and do shift+g then
see if there is a extra line or not.
Sunipa

- End message from "Jefferies D.F." <dfj1...@soton.ac.uk> -
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Re: [gmx-users] Umbrella sampling

[Mark Abraham]

Hi,

Yes, the parsing of that file looks like it doesn't handle blank lines
gracefully, at least. Use a text editor and clean things up. And make sure
the file endings are unix style, e.g. with dos2unix if relevant.

Mark

On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. <dfj1...@soton.ac.uk> wrote:

> Out of curiosity, how did you manage to identify and subsequently remove
> the extra space? I have been having similar problems and the tools I've
> used haven't fixed this problem.
>
> Thanks,
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
> sp...@iacs.res.in [sp...@iacs.res.in]
> Sent: Tuesday, December 19, 2017 6:21 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Umbrella sampling
>
>   - Message from Dhaniram Mahato <bioinfo...@gmail.com> -
> Date: Tue, 19 Dec 2017 21:30:05 +0800
> From: Dhaniram Mahato <bioinfo...@gmail.com>
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Umbrella sampling
>   To: gmx-us...@gromacs.org
>
> > Hi,
> >
> > There could be format problem. You can create your own .dat files by
> > typing
> > it. You have probably copied it from somewhere. I hope it will work then.
> >
> >
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
> >
> > Thanks
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests
> > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or send a mail to gmx-users-requ...@gromacs.org.
>
> Hii
> I have solved the problem. It was just because of one extra space added in
> the tpr-files.dat file. Now its running properly.
>
> - End message from Dhaniram Mahato <bioinfo...@gmail.com> -
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Re: [gmx-users] Umbrella sampling

[Jefferies D . F .]

Out of curiosity, how did you manage to identify and subsequently remove the 
extra space? I have been having similar problems and the tools I've used 
haven't fixed this problem.

Thanks,  

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Tuesday, December 19, 2017 6:21 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

  - Message from Dhaniram Mahato <bioinfo...@gmail.com> -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato <bioinfo...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
  To: gmx-us...@gromacs.org

> Hi,
>
> There could be format problem. You can create your own .dat files by
> typing
> it. You have probably copied it from somewhere. I hope it will work then.
>
>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-requ...@gromacs.org.

Hii
I have solved the problem. It was just because of one extra space added in
the tpr-files.dat file. Now its running properly.

- End message from Dhaniram Mahato <bioinfo...@gmail.com> -
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Re: [gmx-users] Umbrella sampling

[spss4]

 - Message from Dhaniram Mahato <bioinfo...@gmail.com> -
    Date: Tue, 19 Dec 2017 21:30:05 +0800
    From: Dhaniram Mahato <bioinfo...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-us...@gromacs.org


Hi,

There could be format problem. You can create your own .dat files by
typing
it. You have probably copied it from somewhere. I hope it will work then.



https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html


Thanks
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Hii
I have solved the problem. It was just because of one extra space added in
the tpr-files.dat file. Now its running properly.

- End message from Dhaniram Mahato <bioinfo...@gmail.com> -
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Re: [gmx-users] Umbrella sampling

[spss4]

 - Message from Dhaniram Mahato <bioinfo...@gmail.com> -
    Date: Tue, 19 Dec 2017 21:30:05 +0800
    From: Dhaniram Mahato <bioinfo...@gmail.com>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-us...@gromacs.org


Hi,

There could be format problem. You can create your own .dat files by
typing
it. You have probably copied it from somewhere. I hope it will work then.



https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html


Thanks
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Hii
Thanks for replying. I have prepared it by own.I have not copied it.

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Re: [gmx-users] Umbrella sampling

[Dhaniram Mahato]

Hi,

There could be format problem. You can create your own .dat files by typing
it. You have probably copied it from somewhere. I hope it will work then.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html

Thanks
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Re: [gmx-users] Umbrella sampling

[rose rahmani]

On Sat, Dec 16, 2017 at 12:38 PM, rose rahmani 
wrote:

> and also i want protein get closer to ZnS sheet during pulling in just Z
>> direction and straightforward to sheet( like one straight line to sheet),
>> is this suitable md_pull.mdp file for this approach?
>
> is it possible at all?1

> and what about time?is 4nS suitable for each window?
>
>
> Thanks indeed
>
> On Sat, Dec 16, 2017 at 10:05 AM, rose rahmani 
> wrote:
>
>> Hi,
>>
>> I try to use umbrella sampling for calculating PMF. i change distance
>> between protein and ZNS nanosheet. I use gomacsV4.5.4
>>
>> after minimization and equilibration. i use:
>>
>> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
>>
>> this is md_pull.mdp:
>>
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 100
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 500
>> nstlog   = 500
>> nstenergy= 1000
>> nstxtcout= 1000
>> nstlist  = 10
>> rlist= 1.5
>> coulombtype  = pme
>> rcoulomb = 1.5
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> rvdw = 1.2
>> pcoupl   = no
>> gen_vel  = no
>> constraints  = h-bonds
>> ns_type  = grid
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrp-excl   = WAL WAL ZnS ZnS
>> energygrps   = SOL WAL ZnS Protein NA CL
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>>
>> ; Pull code
>> pull= umbrella
>> pull_ngroups= 1
>> pull_group0 = ZnS
>> pull_group1 = Protein
>> pull_geometry   = direction
>> pull_vec1   = 0 0 1
>> pull_dim= N N Y
>> pull_rate1  = -0.01
>> pull_k1 = 5000
>> pull_start  = yes
>> pull_nstxout= 50
>>
>> then: mdrun -s pull.tpr
>> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
>>
>> i got 1000 configuration, i selected 27 of them and foe each of them i
>> run md_umbrella.mdp
>>
>> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p
>> topol.top -n index.ndx -o umbrella0.tpr and then:
>>
>> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>
>>
>>  .This is md_umbrella.mdp file:
>>
>> ntegrator   = md
>> dt   = 0.002
>> nsteps   = 200
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 500
>> nstlog   = 500
>> nstenergy= 1000
>> nstxtcout= 1000
>> nstlist  = 10
>> rlist= 1.5
>> coulombtype  = pme
>> rcoulomb = 1.5
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> rvdw = 1.2
>> pcoupl   = no
>> gen_vel  = no
>> constraints  = h-bonds
>> ns_type  = grid
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrp-excl   = WAL WAL ZnS ZnS
>> energygrps   = SOL WAL ZnS Protein NA CL
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>>
>> pull= umbrella
>> pull_ngroups= 1
>> pull_group0 = ZnS
>> pull_group1 = Protein
>> pull_geometry   = direction
>> pull_vec1   = 0 0 1
>> pull_dim= N N Y
>> pull_rate1  = 0.0; 1 nm per  ns
>> pull_k1 = 5000
>> pull_start  = yes
>> pull_nstxout= 50
>> ...
>>
>> then i use :
>>
>> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>>
>>
>> i get histo.xvg and profile.xvg file but the profile.xvg contains nan 
>> vavlue. i don't know why?
>>
>>
>> # This file was created Wed Dec 13 14:54:35 2017 # by the following
>> command: # g_wham -it tpr-files.dat -if 

Re: [gmx-users] Umbrella sampling

[rose rahmani]

and also i want protein get closer to ZnS sheet during pulling in just Z
direction and straightforward to sheet( like one straight line to sheet),
is this suitable md_pull.mdp file for this approach? and what about time?is
4nS suitable for each window?

Thanks indeed

On Sat, Dec 16, 2017 at 10:05 AM, rose rahmani 
wrote:

> Hi,
>
> I try to use umbrella sampling for calculating PMF. i change distance
> between protein and ZNS nanosheet. I use gomacsV4.5.4
>
> after minimization and equilibration. i use:
>
> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
>
> this is md_pull.mdp:
>
> integrator   = md
> dt   = 0.002
> nsteps   = 100
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 500
> nstlog   = 500
> nstenergy= 1000
> nstxtcout= 1000
> nstlist  = 10
> rlist= 1.5
> coulombtype  = pme
> rcoulomb = 1.5
> vdwtype  = Switch
> rvdw_switch  = 1.0
> rvdw = 1.2
> pcoupl   = no
> gen_vel  = no
> constraints  = h-bonds
> ns_type  = grid
> pbc  = xy
> freezegrps   = WAL ZnS
> freezedim= Y Y Y Y Y Y
> energygrp-excl   = WAL WAL ZnS ZnS
> energygrps   = SOL WAL ZnS Protein NA CL
> nwall= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
>
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_dim= N N Y
> pull_rate1  = -0.01
> pull_k1 = 5000
> pull_start  = yes
> pull_nstxout= 50
>
> then: mdrun -s pull.tpr
> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
>
> i got 1000 configuration, i selected 27 of them and foe each of them i run
> md_umbrella.mdp
>
> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p
> topol.top -n index.ndx -o umbrella0.tpr and then:
>
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>
>
>  .This is md_umbrella.mdp file:
>
> ntegrator   = md
> dt   = 0.002
> nsteps   = 200
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 500
> nstlog   = 500
> nstenergy= 1000
> nstxtcout= 1000
> nstlist  = 10
> rlist= 1.5
> coulombtype  = pme
> rcoulomb = 1.5
> vdwtype  = Switch
> rvdw_switch  = 1.0
> rvdw = 1.2
> pcoupl   = no
> gen_vel  = no
> constraints  = h-bonds
> ns_type  = grid
> pbc  = xy
> freezegrps   = WAL ZnS
> freezedim= Y Y Y Y Y Y
> energygrp-excl   = WAL WAL ZnS ZnS
> energygrps   = SOL WAL ZnS Protein NA CL
> nwall= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
>
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_dim= N N Y
> pull_rate1  = 0.0; 1 nm per  ns
> pull_k1 = 5000
> pull_start  = yes
> pull_nstxout= 50
> ...
>
> then i use :
>
> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>
>
> i get histo.xvg and profile.xvg file but the profile.xvg contains nan vavlue. 
> i don't know why?
>
>
> # This file was created Wed Dec 13 14:54:35 2017 # by the following
> command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
> Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
> (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
> -nan 

Re: [gmx-users] Umbrella sampling

[rose rahmani]

Hi,

I try to use umbrella sampling for calculating PMF. i change distance
between protein and ZNS nanosheet. I use gomacsV4.5.4

after minimization and equilibration. i use:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr

this is md_pull.mdp:

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50

then: mdrun -s pull.tpr
then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep

i got 1000 configuration, i selected 27 of them and foe each of them i run
md_umbrella.mdp

for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top
-n index.ndx -o umbrella0.tpr and then:

mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg


 .This is md_umbrella.mdp file:

ntegrator   = md
dt   = 0.002
nsteps   = 200
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = 0.0; 1 nm per  ns
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
...

then i use :

wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal


i get histo.xvg and profile.xvg file but the profile.xvg contains nan
vavlue. i don't know why?


# This file was created Wed Dec 13 14:54:35 2017 # by the following
command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
# # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
(kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
-nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
-nan 1.265638e+00 -nan

.

.

.

.


Would you please help me? i have not encounter this problem before

Thank you so much

Best regards

Rose




On Mon, Dec 4, 2017 at 1:55 AM, Justin Lemkul  wrote:

>
>
> On 12/3/17 8:42 AM, rose rahmani wrote:
>
>> I need to share you sth which just happened;
>> i run md_pull.mdp in two steps:
>>   1--1nS( dt= 0.001 nsteps=100) ,
>>   2--then i choosed last frame (conf1000.gro) and run it irst time for
>> 2nS(
>> dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001 nsteps=400)

Re: [gmx-users] Umbrella sampling simulation stopped in middle.

[Justin Lemkul]

On 12/4/17 1:33 AM, Sailesh Bataju wrote:

Hi,

I've started to pull a dimer of isobutane molecules as a production md
after npt equilibriation. Here is the md_pull.mdp file for production md.

; Umbrella pulling, production md
; preprocessing parameters
title  = Umbrella Sampling
; run parameters
integrator = md ; leap-frog integrator for integrating Newton's equations
of motion
nsteps = 100 ; 10^6 steps to integrate or maximize i.e. total =
5*10^5*1x10^-15 = 0.5 ns
dt = 0.001 ; time step for integration i.e. 1fs=0.001ps
nstcomm = 100 ; frequency for center of mass motion removal
; output control parameters
nstxout = 1000 ; save coordinates every 1000*1x10^-15 = 1ps
nstvout = 1000 ; save velocities every 1ps
nstenergy = 1000 ; save energies every 1ps
nstfout = 1000 ; number of steps that elapse between writing forces to
output trajectory
nstlog = 1000 ; update log file every 1ps
nstxtcout = 1000 ; gives 1000 frames for umbrella sampling generates .xtc
file
energygrps = Alkane SOL ; groups of the molecules present in the system
that writes to the energy file
; neighbour searching parameters
cutoff-scheme = verlet
nstlist = 10 ; frequency to update neighbour list
ns_type = grid ; search neighboring grid cells
rlist = 1.0 ; Cut-off distance for the short-range neighbor list
pbc = xyz ; periodic boundary conditions in all directions
; electrostatics, vdw and ewald parameters
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 4 ; Interpolation order for PME. 4 equals cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
rcoulomb = 1.0 ; distance for coulomb cut-off
epsilon-r = 1.0 ; relative dielectric constant
rvdw = 1.0 ; distance for the LJ or Buckingham cut-off (short-range van der
waal's cut-off)
optimize_fft = yes
; temperature coupling in on
tcoupl = Nose-Hoover ; modified Berendsen thermostat
tc-grps = Alkane SOL ; groups to couple separately to temperature bath
tau-t = 0.2 0.2 ; time constant for coupling
ref-t = 298 298 ; according to experiment performed before
ld-seed = 1225 ; random seed for temperature
; pressure coupling is on
pcoupl = Parrinello-Rahman ; The box is scaled every timestep,Exponential
relaxation pressure coupling with time constant tau-p
pcoupltype = isotropic
tau-p = 1 ; time constant for coupling in ps
compressibility = 4.6e-5 ; For water at 1 atm at 300K is 4.6e-6bar^(-1)
ref-p = 1 ; reference pressure
refcoord-scaling = com
DispCorr = EnerPres ; apply long range dispersion corrections for Energy
and Pressure
; generate velocity at 298K
gen-vel = no ; generate velocity initially
gen-temp = 298 ; generate temperature for Maxwell distrAlkanetion
gen-seed = 12345 ; given seed
; bonds parameters
continuation = yes ; continue after npt
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
constraint-algorithm = LINCS ; LINear Constraint Solver, holonomic
constraints
; pull code
pull  = yes
pull_coord1_type = umbrella ; Center of mass pulling using an umbrella
potential between the reference group and one or more groups.
pull-ngroups = 2  ; there are two groups that are subject to a biasing
potential
pull-group1-name = IBU_IBU_1 ; The name of the pull group, is looked up in
the index file
pull-group2-name = IBU_IBU_2
pull-coord1-geometry = distance ; pull along the vector connecting the two
groups
pull-ncoords = 1 ; The number of pull coordinates
pull-coord1-groups = 1 2 ; groups 1 and 2 (designated by name above as CA
and CB, respectively) define the reaction coordinate
pull-coord1-k = 840 ; The force constant. For umbrella pulling this is the
harmonic force constant in [kJ mol-1 nm-2]
; 2kcal mol^-1 angostrom^-2 = 840 kJ/mol/nm^2 according to paper
pull-coord1-rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
pull-coord1-dim = Y Y Y ; pulling in all x,y and z direction
pull-coord1-start = yes ; use whatever the distances in the coordinate file
are.

It generated 1000 configuration files without any error. With a separation
of windows of 0.05 nm, i've generated about 23 frames for automated
simulation using python script. All frames went good but last 4 frames
produce error like this:-

Program gmx mdrun, VERSION 5.1.4
Source code file:
/home/akash/Downloads/gromacs-5.1.4/src/gromacs/pulling/pull.cpp,
line: 520

Fatal error:
Distance between pull groups 1 and 2 (1.683443 nm) is larger than 0.49
times the box size (1.717592).
You might want to consider using "pull-geometry = direction-periodic"
instead.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I think this error has to warn us during production md so that future
simulation runs well. Should I change pull-geometry = direction-periodic
(from distance) to continue simulation? If I do so for the remaining 4
frames, does it produce different results (relative to pull-geometry =
distance)? I've no idea what is the best to be done for the last 4 frames.
Considering the time I spent for 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 12/3/17 8:01 AM, rose rahmani wrote:

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:



On 11/28/17 12:23 AM, rose rahmani wrote:


Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?


Bonds can't break and molecules can't "disintegrate" - what you're seeing
is probably a result of PBC.

http://www.gromacs.org/Documentation/Terminology/Periodic_

Boundary_Conditions

I don't know why this doesn't work since yesterday?...anyway...


I used trjconv for just one frame for example conf2000;
trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
whole

so protein turned into to its normal shape, but i'm not sure does it makes
sense or not?! is that right? if it's right, another problem is;
  protein is getting out of box, should i use trjconv for centering?

Thank you for your attentions


A "whole" molecule only matters for visualization. It has no impact on 
physical interactions computed by mdrun.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 12/3/17 8:42 AM, rose rahmani wrote:

I need to share you sth which just happened;
i run md_pull.mdp in two steps:
  1--1nS( dt= 0.001 nsteps=100) ,
  2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001 nsteps=400)
and The protein was in normal shape in EVERY steps!

BUT as i told you before when i run just once in 2nS (dt=0.001
nsteps=200) periodic boundary conditions make the protein look unusual
in for example conf1500.gro?!!!
What happened? I've got really confused?


Read a bit about periodic boundary conditions and what they mean. This 
is normal behavior.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella sampling

[rose rahmani]

I need to share you sth which just happened;
i run md_pull.mdp in two steps:
 1--1nS( dt= 0.001 nsteps=100) ,
 2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001 nsteps=400)
and The protein was in normal shape in EVERY steps!

BUT as i told you before when i run just once in 2nS (dt=0.001
nsteps=200) periodic boundary conditions make the protein look unusual
in for example conf1500.gro?!!!
What happened? I've got really confused?

Thank ou for your attentions

-Rose


On Sun, Dec 3, 2017 at 4:31 PM, rose rahmani  wrote:

>
>
> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>
>>> Hello;
>>>
>>> I took 2000 configuration from trajconv. Amino acid is in its normal
>>> shape
>>> till almost conf1000.gro(and a little more). But in for example
>>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>>> please help me?
>>>
>>
>> Bonds can't break and molecules can't "disintegrate" - what you're seeing
>> is probably a result of PBC.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Bo
>>> undary_Conditions
>>
>> I don't know why this doesn't work since yesterday?...anyway...
>>
> I used trjconv for just one frame for example conf2000;
> trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
> whole
>
> so protein turned into to its normal shape, but i'm not sure does it makes
> sense or not?! is that right? if it's right, another problem is;
>  protein is getting out of box, should i use trjconv for centering?
>
> Thank you for your attentions
>
>
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] Umbrella sampling

[rose rahmani]

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:

>
>
> On 11/28/17 12:23 AM, rose rahmani wrote:
>
>> Hello;
>>
>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>> till almost conf1000.gro(and a little more). But in for example
>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>> please help me?
>>
>
> Bonds can't break and molecules can't "disintegrate" - what you're seeing
> is probably a result of PBC.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
>> Boundary_Conditions
>
> I don't know why this doesn't work since yesterday?...anyway...
>
I used trjconv for just one frame for example conf2000;
trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
whole

so protein turned into to its normal shape, but i'm not sure does it makes
sense or not?! is that right? if it's right, another problem is;
 protein is getting out of box, should i use trjconv for centering?

Thank you for your attentions


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 11/29/17 2:45 PM, rose rahmani wrote:

Hello;

would you please send me Mr.lemkul's article link ? i can't find them.


It's linked here: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html


If you need something regarding my published research, contact me 
directly. This really has nothing to do with GROMACS.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani  wrote:

>
>
> On Mon, Nov 27, 2017 at 1:55 AM, Alex  wrote:
>
>> Hi,
>>
>> The answer is clearly in the error, just read it please:
>> 2.848793 > 0.49 * (4/2) where 4 is the box length.
>>
>>> But i choose ( by pull_coord1_dim) Z direction for pulling (12 nm not
>>> 4nm), it doesn't mean that protein should just get closer to ZnS(sheet) in
>>> Z direction?
>>
>>  thank you so much
>>
>>
>>
>> You can either keep the “pull_coord1_geometry= distance” and increase
>> the box length or change the “pull_coord1_geometry” to  “=
>> direction-periodic“. I prefer the former though.
>>
>> Cheers,
>> Alex
>>
>>> I've got it.
>>
>> would you please answer to another questions too? thank you in advance
>>
>>
>
>>
>>
>> On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:
>>
>> > Hi;
>> >
>> > This is md_pull.mdp
>> >
>> > integrator   = md
>> > dt   = 0.001
>> > nsteps   = 200
>> > nstxout  = 0
>> > nstvout  = 0
>> > nstfout  = 0
>> > nstlog   = 500
>> > nstenergy= 1000
>> > nstxtcout= 1000
>> > rlist= 1.5
>> > rcoulomb = 1.5
>> > rvdw = 1.2
>> > coulombtype  = pme
>> > cutoff-scheme= group
>> > vdwtype  = Switch
>> > rvdw_switch  = 1.0
>> > pcoupl   = no
>> > gen-vel  = yes
>> > gen-temp = 0
>> > gen-seed = 173529
>> > constraints  = h-bonds
>> > pbc  = xy
>> > freezegrps   = WAL ZnS
>> > freezedim= Y Y Y Y Y Y
>> > energygrp-excl   = WAL WAL ZnS ZnS
>> > energygrps   = SOL WAL ZnS Protein NA CL
>> > nwall= 2
>> > wall-atomtype= C C
>> > wall-type= 9-3
>> > wall-density = 150 150
>> > wall-ewald-zfac  = 3
>> > ewald-geometry   = 3dc
>> > fourierspacing   = 0.12
>> > tcoupl   = v-rescale
>> > tc-grps  = System
>> > tau-t= 0.1
>> > ref-t= 300
>> > pull= yes
>> > pull_ngroups= 2
>> > pull_ncoords= 1
>> > pull_group1_name= ZnS
>> > pull_group2_name= Protein
>> > pull_coord1_type= umbrella
>> > pull_coord1_geometry= distance
>> > pull_coord1_groups  = 1 2
>> > pull__coord1_dim= N N Y
>> > pull_coord1_rate  = -0.001; 1 nm per  ns
>> > pull_coord1_k = 5000
>> > pull_coord1_start  = yes
>> >
>> > Program gmx grompp, VERSION 5.1.4
>> >
>> > Fatal error:
>> > Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
>> > times the box size (2.00).
>> > You might want to consider using "pull-geometry = direction-periodic"
>> > instead.
>> >
>> > the box size is= 4 4 12
>> >
>> > could you please help me to resolve it?
>> > -
>> > Mr.Lemkul told me rcutt-off is wrong and
>> >
>> >  i should'nt put "cutoff-scheme= group" >>>but when i remove
>> > it i'll get  this error too;
>> >
>> >   >>With Verlet lists rcoulomb!=rvdw is not supported
>> >
>> > i know it's wrong solution but what is my alternative?!!
>> >
>> > --
>> > -dummy particle should move towards the surface with a constant speed
>> of 1
>> > nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
>> > corresponding to the spring constant of 5000.
>> >
>> > I DON'T know how should i implement deltaZ(=2)? which .mdp option
>> refers to
>> > it?!
>> >
>> > thank you so much
>> >
>> > Best regards
>> > Rose
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
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>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
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>
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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/28/17 10:00 AM, rose rahmani wrote:

Would "pull_geometry=periodic-distance" be another solution for it?


No. That affects how the reaction coordinate distance is calculated, not 
the PBC treatment, which is intrinsic to any simulation using PBC.


-Justin


On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:



On 11/28/17 12:23 AM, rose rahmani wrote:


Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?


Bonds can't break and molecules can't "disintegrate" - what you're seeing
is probably a result of PBC.

http://www.gromacs.org/Documentation/Terminology/Periodic_
Boundary_Conditions


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella sampling

[rose rahmani]

Would "pull_geometry=periodic-distance" be another solution for it?

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:

>
>
> On 11/28/17 12:23 AM, rose rahmani wrote:
>
>> Hello;
>>
>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>> till almost conf1000.gro(and a little more). But in for example
>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>> please help me?
>>
>
> Bonds can't break and molecules can't "disintegrate" - what you're seeing
> is probably a result of PBC.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
> Boundary_Conditions
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/28/17 12:23 AM, rose rahmani wrote:

Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?


Bonds can't break and molecules can't "disintegrate" - what you're 
seeing is probably a result of PBC.


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] Umbrella sampling

[rose rahmani]

Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?

Best regards
Rose

On Sun, Nov 26, 2017 at 12:39 AM, Justin Lemkul  wrote:

>
>
> On 11/25/17 3:59 PM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 3:07 PM, rose rahmani wrote:
>>>
>>> Oh sorry this is .mdp file:

 DEFINE   = -DPOSRES

 What are you restraining? This seems counterproductive, and by default
>>>
 (unless you've hacked the topology), this is going to restrain your
 protein, which is definitely wrong.

>>> yes, protein.you mean i should remove it and don't restraint anything?
>>> and
>>> for npt(previous step) run too?
>>>
>>
> What is the purpose of a restraint? To prevent motion. What is your
> objective? To cause motion of your protein towards a surface. Does it make
> sense to restrain the protein during this process?
>
> Equilibration is a separate matter.
>
> integrator   = md
 dt   = 0.001
 nsteps   = 200
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 500
 nstenergy= 1000
 nstxtcout= 1000
 rlist= 1.5
 rcoulomb = 1.5
 rvdw = 1.2

 Again, I am suspicious of these cutoffs. What force field are you using?
>>>
>>> AMBER99
>>>
>>
> Then yes, those cutoffs are wrong. This is also a very old force field,
> and newer/better variants of it exist. Refer to the literature to find the
> right cutoffs for the parameter set you decide upon. This is not a trivial
> matter.
>
>
> coulombtype  = pme
>>>
 cutoff-scheme= group
 vdwtype  = Switch
 rvdw_switch  = 1.0
 pcoupl   = no
 gen-vel  = yes
 gen-temp = 0
 gen-seed = 173529
 constraints  = h-bonds
 pbc  = xy
 freezegrps   = WAL ZnS
 freezedim= Y Y Y Y Y Y
 energygrp-excl   = WAL WAL ZnO ZnO
 energygrps   = SOL WAL ZnO Protein NA CL
 nwall= 2
 wall-atomtype= C C
 wall-type= 9-3
 wall-density = 150 150
 wall-ewald-zfac  = 3
 ewald-geometry   = 3dc
 fourierspacing   = 0.12
 tcoupl   = v-rescale
 tc-grps  = System
 tau-t= 0.1
 ref-t= 300
 pull= yes
 pull_ngroups= 2
 pull_ncoords= 1
 pull_group1_name= ZnS
 pull_group2_name= Protein-H

 You can probably just use the whole protein here, though I doubt it
>>> makes
>>> much difference.
>>>
>>> pull_coord1_type= umbrella  ; harmonic biasing force
>>>
 pull_coord1_geometry= distance  ; simple distance increase
 pull_coord1_groups  = 1 2
 pull_coord1_dim = N N Y
 pull_coord1_rate= 0.001

 Here's your problem. With a positive pull rate, you are instructing
>>> mdrun
>>>
 to increase the COM distance between the protein and the ZnS surface. If
 you want them to come closer, you need a negative value here, to
 decrease
 the distance as a function of time. Of course, this all goes out the
 window
 if your protein is restrained, as suggested above.

>>>
>>> oh, i've got it.
>> you restrained chain B in tutorial but i shouldn't because ZnS is freezed?
>>
>
> No, I restrained a chain in my protein to mimic the stability of
> (physiologically) much larger systems. People typically fail to read my
> paper that is the basis of that tutorial, in which this concept is
> explained. Perhaps I need to add a bold, flashing warning that people
> should not be blindly following the method.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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> 

Re: [gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 1:55 AM, Alex  wrote:

> Hi,
>
> The answer is clearly in the error, just read it please:
> 2.848793 > 0.49 * (4/2) where 4 is the box length.
>
> You can either keep the “pull_coord1_geometry= distance” and increase
> the box length or change the “pull_coord1_geometry” to  “=
> direction-periodic“. I prefer the former though.
>
> Cheers,
> Alex
>
>> I've got it.
>
> would you please answer to another questions too? thank you in advance
>
>

>
>
> On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:
>
> > Hi;
> >
> > This is md_pull.mdp
> >
> > integrator   = md
> > dt   = 0.001
> > nsteps   = 200
> > nstxout  = 0
> > nstvout  = 0
> > nstfout  = 0
> > nstlog   = 500
> > nstenergy= 1000
> > nstxtcout= 1000
> > rlist= 1.5
> > rcoulomb = 1.5
> > rvdw = 1.2
> > coulombtype  = pme
> > cutoff-scheme= group
> > vdwtype  = Switch
> > rvdw_switch  = 1.0
> > pcoupl   = no
> > gen-vel  = yes
> > gen-temp = 0
> > gen-seed = 173529
> > constraints  = h-bonds
> > pbc  = xy
> > freezegrps   = WAL ZnS
> > freezedim= Y Y Y Y Y Y
> > energygrp-excl   = WAL WAL ZnS ZnS
> > energygrps   = SOL WAL ZnS Protein NA CL
> > nwall= 2
> > wall-atomtype= C C
> > wall-type= 9-3
> > wall-density = 150 150
> > wall-ewald-zfac  = 3
> > ewald-geometry   = 3dc
> > fourierspacing   = 0.12
> > tcoupl   = v-rescale
> > tc-grps  = System
> > tau-t= 0.1
> > ref-t= 300
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 1
> > pull_group1_name= ZnS
> > pull_group2_name= Protein
> > pull_coord1_type= umbrella
> > pull_coord1_geometry= distance
> > pull_coord1_groups  = 1 2
> > pull__coord1_dim= N N Y
> > pull_coord1_rate  = -0.001; 1 nm per  ns
> > pull_coord1_k = 5000
> > pull_coord1_start  = yes
> >
> > Program gmx grompp, VERSION 5.1.4
> >
> > Fatal error:
> > Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> > times the box size (2.00).
> > You might want to consider using "pull-geometry = direction-periodic"
> > instead.
> >
> > the box size is= 4 4 12
> >
> > could you please help me to resolve it?
> > -
> > Mr.Lemkul told me rcutt-off is wrong and
> >
> >  i should'nt put "cutoff-scheme= group" >>>but when i remove
> > it i'll get  this error too;
> >
> >   >>With Verlet lists rcoulomb!=rvdw is not supported
> >
> > i know it's wrong solution but what is my alternative?!!
> >
> > --
> > -dummy particle should move towards the surface with a constant speed of
> 1
> > nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> > corresponding to the spring constant of 5000.
> >
> > I DON'T know how should i implement deltaZ(=2)? which .mdp option refers
> to
> > it?!
> >
> > thank you so much
> >
> > Best regards
> > Rose
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] umbrella sampling

[Alex]

Hi,

The answer is clearly in the error, just read it please:
2.848793 > 0.49 * (4/2) where 4 is the box length.

You can either keep the “pull_coord1_geometry= distance” and increase
the box length or change the “pull_coord1_geometry” to  “=
direction-periodic“. I prefer the former though.

Cheers,
Alex

On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:

> Hi;
>
> This is md_pull.mdp
>
> integrator   = md
> dt   = 0.001
> nsteps   = 200
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 500
> nstenergy= 1000
> nstxtcout= 1000
> rlist= 1.5
> rcoulomb = 1.5
> rvdw = 1.2
> coulombtype  = pme
> cutoff-scheme= group
> vdwtype  = Switch
> rvdw_switch  = 1.0
> pcoupl   = no
> gen-vel  = yes
> gen-temp = 0
> gen-seed = 173529
> constraints  = h-bonds
> pbc  = xy
> freezegrps   = WAL ZnS
> freezedim= Y Y Y Y Y Y
> energygrp-excl   = WAL WAL ZnS ZnS
> energygrps   = SOL WAL ZnS Protein NA CL
> nwall= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> pull= yes
> pull_ngroups= 2
> pull_ncoords= 1
> pull_group1_name= ZnS
> pull_group2_name= Protein
> pull_coord1_type= umbrella
> pull_coord1_geometry= distance
> pull_coord1_groups  = 1 2
> pull__coord1_dim= N N Y
> pull_coord1_rate  = -0.001; 1 nm per  ns
> pull_coord1_k = 5000
> pull_coord1_start  = yes
>
> Program gmx grompp, VERSION 5.1.4
>
> Fatal error:
> Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> times the box size (2.00).
> You might want to consider using "pull-geometry = direction-periodic"
> instead.
>
> the box size is= 4 4 12
>
> could you please help me to resolve it?
> -
> Mr.Lemkul told me rcutt-off is wrong and
>
>  i should'nt put "cutoff-scheme= group" >>>but when i remove
> it i'll get  this error too;
>
>   >>With Verlet lists rcoulomb!=rvdw is not supported
>
> i know it's wrong solution but what is my alternative?!!
>
> --
> -dummy particle should move towards the surface with a constant speed of 1
> nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> corresponding to the spring constant of 5000.
>
> I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
> it?!
>
> thank you so much
>
> Best regards
> Rose
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 11/26/17 1:08 PM, Roja wrote:

Would you please tell me what is the difference between using umbrella in 4.5.x 
version and 5.1.4 version?are they different in ACCURACY of sampling?


Probably. There have been thousands of bug fixes and features added 
since 4.5.4, which was released 6 years ago. Refer to any and all of the 
release notes in the 4.5.x, 4.6.x, 5.0.x, 5.1.x, and 2016.x series. 
Again, the 4.5.x series is deprecated and officially unsupported.


-Justin


Sent from my iPhone


On Nov 26, 2017, at 21:14, Justin Lemkul  wrote:




On 11/26/17 12:40 PM, rose rahmani wrote:
Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?

Why use deprecated software? We don't officially support the 4.5.x series any 
more. Use the newest version. Some things don't have exact equivalents because 
the pull code was completely re-written a few years ago.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella Sampling

[Roja]

Would you please tell me what is the difference between using umbrella in 4.5.x 
version and 5.1.4 version?are they different in ACCURACY of sampling?

Sent from my iPhone

> On Nov 26, 2017, at 21:14, Justin Lemkul  wrote:
> 
> 
> 
>> On 11/26/17 12:40 PM, rose rahmani wrote:
>> Hello;
>> 
>> what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) 
>> called in version 4.5.4?
> 
> Why use deprecated software? We don't officially support the 4.5.x series any 
> more. Use the newest version. Some things don't have exact equivalents 
> because the pull code was completely re-written a few years ago.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==
> 
> -- 
> Gromacs Users mailing list
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 11/26/17 12:40 PM, rose rahmani wrote:

Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?


Why use deprecated software? We don't officially support the 4.5.x 
series any more. Use the newest version. Some things don't have exact 
equivalents because the pull code was completely re-written a few years ago.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/25/17 3:59 PM, rose rahmani wrote:

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul  wrote:



On 11/25/17 3:07 PM, rose rahmani wrote:


Oh sorry this is .mdp file:

DEFINE   = -DPOSRES


What are you restraining? This seems counterproductive, and by default

(unless you've hacked the topology), this is going to restrain your
protein, which is definitely wrong.

yes, protein.you mean i should remove it and don't restraint anything? and
for npt(previous step) run too?


What is the purpose of a restraint? To prevent motion. What is your 
objective? To cause motion of your protein towards a surface. Does it 
make sense to restrain the protein during this process?


Equilibration is a separate matter.


integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2


Again, I am suspicious of these cutoffs. What force field are you using?

AMBER99


Then yes, those cutoffs are wrong. This is also a very old force field, 
and newer/better variants of it exist. Refer to the literature to find 
the right cutoffs for the parameter set you decide upon. This is not a 
trivial matter.



coulombtype  = pme

cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H


You can probably just use the whole protein here, though I doubt it makes
much difference.

pull_coord1_type= umbrella  ; harmonic biasing force

pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001


Here's your problem. With a positive pull rate, you are instructing mdrun

to increase the COM distance between the protein and the ZnS surface. If
you want them to come closer, you need a negative value here, to decrease
the distance as a function of time. Of course, this all goes out the window
if your protein is restrained, as suggested above.



oh, i've got it.
you restrained chain B in tutorial but i shouldn't because ZnS is freezed?


No, I restrained a chain in my protein to mimic the stability of 
(physiologically) much larger systems. People typically fail to read my 
paper that is the basis of that tutorial, in which this concept is 
explained. Perhaps I need to add a bold, flashing warning that people 
should not be blindly following the method.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella sampling

[rose rahmani]

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 3:07 PM, rose rahmani wrote:
>
>> Oh sorry this is .mdp file:
>>
>> DEFINE   = -DPOSRES
>>
>
> What are you restraining? This seems counterproductive, and by default
>> (unless you've hacked the topology), this is going to restrain your
>> protein, which is definitely wrong.
>
> yes, protein.you mean i should remove it and don't restraint anything? and
> for npt(previous step) run too?
>
>> integrator   = md
>> dt   = 0.001
>> nsteps   = 200
>> nstxout  = 0
>> nstvout  = 0
>> nstfout  = 0
>> nstlog   = 500
>> nstenergy= 1000
>> nstxtcout= 1000
>> rlist= 1.5
>> rcoulomb = 1.5
>> rvdw = 1.2
>>
>
> Again, I am suspicious of these cutoffs. What force field are you using?
>
> AMBER99
>
> coulombtype  = pme
>> cutoff-scheme= group
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> pcoupl   = no
>> gen-vel  = yes
>> gen-temp = 0
>> gen-seed = 173529
>> constraints  = h-bonds
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrp-excl   = WAL WAL ZnO ZnO
>> energygrps   = SOL WAL ZnO Protein NA CL
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= ZnS
>> pull_group2_name= Protein-H
>>
>
> You can probably just use the whole protein here, though I doubt it makes
> much difference.
>
> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.001
>>
>
> Here's your problem. With a positive pull rate, you are instructing mdrun
>> to increase the COM distance between the protein and the ZnS surface. If
>> you want them to come closer, you need a negative value here, to decrease
>> the distance as a function of time. Of course, this all goes out the window
>> if your protein is restrained, as suggested above.
>
>
oh, i've got it.
you restrained chain B in tutorial but i shouldn't because ZnS is freezed?


> -Justin
>
>
> pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>>
>> On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 11:49 AM, rose rahmani wrote:
>>>
>>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:


 On 11/24/17 3:32 PM, rose rahmani wrote:
>
> I attached md_pull.mdp file
>
>> i put " cutoff-scheme = group" beecause of some errors (about energy
>> groups)
>>
>> The use of energygrps has no effect on the physics. You should view
>>
> pairwise interactions energies as an analysis method, not something
> that
> you need to do as part of your MD run. Don't base your algorithm
> choices
> on
> a quantity that is usually meaningless.
>
> This is what i try to do(part of some literatures);
>
> 1-pulling the CM of the object along the z-axis—perpendicular to the
>> surface of ZnO
>>
>> 2-Pulling is implemented through a “dummy particle” which moves
>> towards
>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>> and drags the CM by the harmonic force corresponding to the spring
>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>> the PMF is averaged laterally
>>
>> 3-The conformations are scanned every 0.1 ps in order to save them
>> with the CM within each of the interval of width 0.05 nm. ( most of
>> all i'm not sure about this part of my mdp file and i don't know how
>> should i implement them).
>>
>> I don't know what .mdp setting you're referring to here.
>>
> Sorry, I didn't understand what you mean?
>
> The mailing list does not accept attachments, so your .mdp file did not
>>> come through. I'm working blind on what settings you're using. What I
>>> specifically don't understand here is your connection between the desired
>>> spacing along the reaction coordinate and whatever .mdp settings you
>>> think
>>> 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/25/17 3:07 PM, rose rahmani wrote:

Oh sorry this is .mdp file:

DEFINE   = -DPOSRES


What are you restraining? This seems counterproductive, and by default 
(unless you've hacked the topology), this is going to restrain your 
protein, which is definitely wrong.



integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2


Again, I am suspicious of these cutoffs. What force field are you using?


coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H


You can probably just use the whole protein here, though I doubt it 
makes much difference.



pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001


Here's your problem. With a positive pull rate, you are instructing 
mdrun to increase the COM distance between the protein and the ZnS 
surface. If you want them to come closer, you need a negative value 
here, to decrease the distance as a function of time. Of course, this 
all goes out the window if your protein is restrained, as suggested above.


-Justin


pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul  wrote:



On 11/25/17 11:49 AM, rose rahmani wrote:


On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:



On 11/24/17 3:32 PM, rose rahmani wrote:

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy
groups)

The use of energygrps has no effect on the physics. You should view

pairwise interactions energies as an analysis method, not something that
you need to do as part of your MD run. Don't base your algorithm choices
on
a quantity that is usually meaningless.

This is what i try to do(part of some literatures);


1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).

I don't know what .mdp setting you're referring to here.

Sorry, I didn't understand what you mean?


The mailing list does not accept attachments, so your .mdp file did not
come through. I'm working blind on what settings you're using. What I
specifically don't understand here is your connection between the desired
spacing along the reaction coordinate and whatever .mdp settings you think
affect this. You can only tell mdrun how frequently to save a frame, you
can't tell it anything about the interval along the reaction coordinate you
care about. Save coordinates frequently enough that you can plausibly
generate a set of configurations to use.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? 

Re: [gmx-users] umbrella sampling

[rose rahmani]

Oh sorry this is .mdp file:

DEFINE   = -DPOSRES
integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnO
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001
pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0




On Sat, Nov 25, 2017 at 11:31 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 12:57 PM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 5:05 AM, rose rahmani wrote:
>>>
>>> Hi,

 i'm using umbrella sampling and i'm a beginner in GROMACS.

 as an example i got 5 dist.xvg files and then:

 command: perl  distances.pl

> this is distances.pl:
>
 #!/usr/bin/perl -w
 use strict;


 # write output to single file
 open(OUT, ">>summary_distances.dat");

 for (my $j=0; $j<=5; $j++) {
open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91>
 <9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
 #
 @title "Distance"
 @xaxis  label "Time (ps)"
 @yaxis  label "Distance (nm)"
 @TYPE xy
 0.0000.3820.3820.3830.3830.3830.383
 1.178
 0.3820.3820.3830.3830.3830.3830.3830.382
 0.8180.3820.3820.3820.3820.5410.5410.541
 0.5410.5410.5410.5410.5410.5410.5410.541
 0.5410.5410.5410.5410.5410.5410.5410.541
 0.5410.5410.5410.5410.541

Re: [gmx-users] Umbrella sampling

[rose rahmani]

Oh sorry this is .mdp file:

DEFINE   = -DPOSRES
integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001
pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 11:49 AM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>>
>>> I attached md_pull.mdp file

 i put " cutoff-scheme = group" beecause of some errors (about energy
 groups)

 The use of energygrps has no effect on the physics. You should view
>>> pairwise interactions energies as an analysis method, not something that
>>> you need to do as part of your MD run. Don't base your algorithm choices
>>> on
>>> a quantity that is usually meaningless.
>>>
>>> This is what i try to do(part of some literatures);
>>>
 1-pulling the CM of the object along the z-axis—perpendicular to the
 surface of ZnO

 2-Pulling is implemented through a “dummy particle” which moves towards
 the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
 and drags the CM by the harmonic force corresponding to the spring
 constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
 the PMF is averaged laterally

 3-The conformations are scanned every 0.1 ps in order to save them
 with the CM within each of the interval of width 0.05 nm. ( most of
 all i'm not sure about this part of my mdp file and i don't know how
 should i implement them).

 I don't know what .mdp setting you're referring to here.
>>>
>>> Sorry, I didn't understand what you mean?
>>>
>>
> The mailing list does not accept attachments, so your .mdp file did not
> come through. I'm working blind on what settings you're using. What I
> specifically don't understand here is your connection between the desired
> spacing along the reaction coordinate and whatever .mdp settings you think
> affect this. You can only tell mdrun how frequently to save a frame, you
> can't tell it anything about the interval along the reaction coordinate you
> care about. Save coordinates frequently enough that you can plausibly
> generate a set of configurations to use.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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mail to 

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 11/25/17 12:57 PM, rose rahmani wrote:

On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul  wrote:



On 11/25/17 5:05 AM, rose rahmani wrote:


Hi,

i'm using umbrella sampling and i'm a beginner in GROMACS.

as an example i got 5 dist.xvg files and then:

command: perl  distances.pl

this is distances.pl:

#!/usr/bin/perl -w
use strict;


# write output to single file
open(OUT, ">>summary_distances.dat");

for (my $j=0; $j<=5; $j++) {
   open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91>
<9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
0.0000.3820.3820.3830.3830.3830.383
1.178
0.3820.3820.3830.3830.3830.3830.3830.382
0.8180.3820.3820.3820.3820.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.3820.3820.383
0.3830.3830.3831.1780.3820.3820.3830.383
0.3830.3830.3830.3820.8180.3820.3820.382
0.3820.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.1510.2370.1600.2420.1230.147
~
~

what is my mistake?is that perl script or?! or because of i selected very
close conf.gro files (0-5)?


My Perl script expects each file to have *one* value in it, the COM
distance between two chosen groups. Your output seems to be something else
entirely, suggesting you didn't choose 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/25/17 11:49 AM, rose rahmani wrote:

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:



On 11/24/17 3:32 PM, rose rahmani wrote:


I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy
groups)


The use of energygrps has no effect on the physics. You should view
pairwise interactions energies as an analysis method, not something that
you need to do as part of your MD run. Don't base your algorithm choices on
a quantity that is usually meaningless.

This is what i try to do(part of some literatures);

1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).


I don't know what .mdp setting you're referring to here.

Sorry, I didn't understand what you mean?


The mailing list does not accept attachments, so your .mdp file did not 
come through. I'm working blind on what settings you're using. What I 
specifically don't understand here is your connection between the 
desired spacing along the reaction coordinate and whatever .mdp settings 
you think affect this. You can only tell mdrun how frequently to save a 
frame, you can't tell it anything about the interval along the reaction 
coordinate you care about. Save coordinates frequently enough that you 
can plausibly generate a set of configurations to use.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] umbrella sampling

[rose rahmani]

On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 5:05 AM, rose rahmani wrote:
>
>> Hi,
>>
>> i'm using umbrella sampling and i'm a beginner in GROMACS.
>>
>> as an example i got 5 dist.xvg files and then:
>>
>> command: perl  distances.pl

>>> this is distances.pl:
>> #!/usr/bin/perl -w
>>use strict;
>>
>>
>># write output to single file
>>open(OUT, ">>summary_distances.dat");
>>
>>for (my $j=0; $j<=5; $j++) {
>>   open(IN, ">   my @array = ;
>>
>>  my $distance;
>>
>>   foreach $_ (@array) {
>>   if ($_ =~ /[#@]/) {
>>   # do nothing, it's a comment
>> or formatting line
>>   } else {
>>   my
>> @line =
>> split(" ", $_);
>>
>>   $distance = $line[1];
>>
>>   }
>>
>>   }
>>
>>
>>   close(IN);
>>
>>   print OUT "$j\t$distance\n";
>>
>>   }
>>
>>
>>   close(OUT);
>>
>>
>>   # clean up
>>
>>   print "Cleaning up...\n";
>>
>>
>>   for (my $k=0; $k<=5; $k++) {
>>
>>   unlink "dist${k}.xvg";
>>
>>   }
>>
>>
>>  exit;
>>
>> but summary-distances.dat:
>>
>> 0   0.382
>> 1   0.382
>> 0   0.382
>> 1   0.382
>> 2   0.382
>> 3   0.382
>> 4   0.382
>> 5   0.382
>> ~
>> ~
>> ~
>>
>> 0.382 is just the first number in dist.xvg files;
>>
>> for example dist0.xvg is:
>>
>> # This file was created Sat Nov 25 04:47:25 2017
>> # Created by:
>> # :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
>> #
>> # Executable:   /usr/local/gromacs/bin/gmx
>> # Data prefix:  /usr/local/gromacs
>> # Command line:
>> #   gmx distance -s pull.tpr -f conf0.gro -n index.ndx -oall dist0.xvg
>> # gmx distance is part of G R O M A C S:
>> #
>> #
>> ¸­°<88><96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91>
>> <9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
>> #
>> @title "Distance"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Distance (nm)"
>> @TYPE xy
>>0.0000.3820.3820.3830.3830.3830.383
>> 1.178
>>0.3820.3820.3830.3830.3830.3830.3830.382
>> 0.8180.3820.3820.3820.3820.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.3820.3820.383
>> 0.3830.3830.3831.1780.3820.3820.3830.383
>> 0.3830.3830.3830.3820.8180.3820.3820.382
>> 0.3820.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.1510.2370.1600.2420.123

Re: [gmx-users] Umbrella sampling

[rose rahmani]

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:

>
>
> On 11/24/17 3:32 PM, rose rahmani wrote:
>
>> I attached md_pull.mdp file
>>
>> i put " cutoff-scheme = group" beecause of some errors (about energy
>> groups)
>>
>
> The use of energygrps has no effect on the physics. You should view
> pairwise interactions energies as an analysis method, not something that
> you need to do as part of your MD run. Don't base your algorithm choices on
> a quantity that is usually meaningless.
>
> This is what i try to do(part of some literatures);
>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>> surface of ZnO
>>
>> 2-Pulling is implemented through a “dummy particle” which moves towards
>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>> and drags the CM by the harmonic force corresponding to the spring
>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>> the PMF is averaged laterally
>>
>> 3-The conformations are scanned every 0.1 ps in order to save them
>> with the CM within each of the interval of width 0.05 nm. ( most of
>> all i'm not sure about this part of my mdp file and i don't know how
>> should i implement them).
>>
>
> I don't know what .mdp setting you're referring to here.
>
> Sorry, I didn't understand what you mean?

>
> 4-between 36-38 conformations should be collected and i dont know how
>> should i choose them between 710 conf.gro files( i got 710
>> conformations after using trajconv)
>>
>
> Calculate the COM distance between the groups for each frame. This is what
> my tutorial does and what my provided scripts help you to analyze. Compile
> a list of the COM distances and determine which frames are suitable for
> starting points of each window.
>
> -Justin
>
>
> this is first part of my job.
>>
>> protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.
>>
>> what do you think about mdp file? where did i make a mistake?
>>
>> Thank you for your attentions (like always ;) )
>>
>> Best Regards
>>
>>
>>
>>
>>
>> Sent from my iPhone
>>
>> On Nov 24, 2017, at 19:34, Justin Lemkul  wrote:
>>>
>>>
>>>
>>> On 11/24/17 9:14 AM, Rose wrote:
 Hello

 I'm beginner in GROMACS. I'm using umbrella sampling(helping from its
 tutorial with MR Lemkul) But I don't know how should I implement deltaZ and
 how choose different conf.gro and which will be useful for further 
 sampling.
 To tell the truth I couldn't get summary.dat by "perl distance.pl"
 command.as I'm not good in programming I couldn't understand what
 happened there?!

>>> Run gmx distance manually. It's probably returning some error, so the
>>> script fails. I've heard this reported a number of times and no one's ever
>>> told me what the solution is, so unfortunately there's nothing I can do to
>>> fix it.
>>>
>>> How did you know for example:
 50>>>0.6 nm
 100>>>0.8 nm

>>> This is what gmx distance computes.
>>>
>>> I need deltaz=0.05nm

>>> Then you will need to save frames very frequently. This is a very narrow
>>> dz, and may be overkill depending on what the system is.
>>>
>>> Please help me, i don't know where should i find these informations and
 modify them.

 2- I want that reaction coordinate across Z axes, from slab to 1.5nm
 far from it (and rvdw and coulomb=1.5 and

>>> What force field uses such a cutoff? Don't make ad hoc changes to the
>>> cutoffs used by any given force field, as you will get unexpected (or
>>> invalid) results...
>>>
>>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer
 to wall(4nm far from slab) except slab.
 What is my mistake?!

>>> You'll have to provide an .mdp file and a complete description of your
>>> system, how you constructed it, and what your objectives are. Images would
>>> help.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> 

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 11/25/17 5:05 AM, rose rahmani wrote:

Hi,

i'm using umbrella sampling and i'm a beginner in GROMACS.

as an example i got 5 dist.xvg files and then:


command: perl  distances.pl

this is distances.pl:
#!/usr/bin/perl -w
   use strict;


   # write output to single file
   open(OUT, ">>summary_distances.dat");

   for (my $j=0; $j<=5; $j++) {
  open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91><9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
   0.0000.3820.3820.3830.3830.3830.3831.178
   0.3820.3820.3830.3830.3830.3830.3830.382
0.8180.3820.3820.3820.3820.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.3820.3820.383
0.3830.3830.3831.1780.3820.3820.3830.383
0.3830.3830.3830.3820.8180.3820.3820.382
0.3820.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.1510.2370.1600.2420.1230.147
~
~

what is my mistake?is that perl script or?! or because of i selected very
close conf.gro files (0-5)?


My Perl script expects each file to have *one* value in it, the COM 
distance between two chosen groups. Your output seems to be something 
else entirely, suggesting you didn't choose appropriate groups.



i selected them just for testing my script and to tell the truth i didn't
know how use gmx distance to get all 718 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/24/17 3:32 PM, rose rahmani wrote:

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy groups)


The use of energygrps has no effect on the physics. You should view 
pairwise interactions energies as an analysis method, not something that 
you need to do as part of your MD run. Don't base your algorithm choices 
on a quantity that is usually meaningless.



This is what i try to do(part of some literatures);
1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).


I don't know what .mdp setting you're referring to here.


4-between 36-38 conformations should be collected and i dont know how
should i choose them between 710 conf.gro files( i got 710
conformations after using trajconv)


Calculate the COM distance between the groups for each frame. This is 
what my tutorial does and what my provided scripts help you to analyze. 
Compile a list of the COM distances and determine which frames are 
suitable for starting points of each window.


-Justin


this is first part of my job.

protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.

what do you think about mdp file? where did i make a mistake?

Thank you for your attentions (like always ;) )

Best Regards





Sent from my iPhone


On Nov 24, 2017, at 19:34, Justin Lemkul  wrote:




On 11/24/17 9:14 AM, Rose wrote:
Hello

I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial 
with MR Lemkul) But I don't know how should I implement deltaZ and how choose 
different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as 
I'm not good in programming I couldn't understand what happened there?!

Run gmx distance manually. It's probably returning some error, so the script 
fails. I've heard this reported a number of times and no one's ever told me 
what the solution is, so unfortunately there's nothing I can do to fix it.


How did you know for example:
50>>>0.6 nm
100>>>0.8 nm

This is what gmx distance computes.


I need deltaz=0.05nm

Then you will need to save frames very frequently. This is a very narrow dz, 
and may be overkill depending on what the system is.


Please help me, i don't know where should i find these informations and modify 
them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from 
it (and rvdw and coulomb=1.5 and

What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs 
used by any given force field, as you will get unexpected (or invalid) 
results...


rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to 
wall(4nm far from slab) except slab.
What is my mistake?!

You'll have to provide an .mdp file and a complete description of your system, 
how you constructed it, and what your objectives are. Images would help.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Umbrella sampling

[rose rahmani]

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy groups)

This is what i try to do(part of some literatures);
1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).

4-between 36-38 conformations should be collected and i dont know how
should i choose them between 710 conf.gro files( i got 710
conformations after using trajconv)

this is first part of my job.

protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.

what do you think about mdp file? where did i make a mistake?

Thank you for your attentions (like always ;) )

Best Regards





Sent from my iPhone

> On Nov 24, 2017, at 19:34, Justin Lemkul  wrote:
>
>
>
>> On 11/24/17 9:14 AM, Rose wrote:
>> Hello
>>
>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its 
>> tutorial with MR Lemkul) But I don't know how should I implement deltaZ and 
>> how choose different conf.gro and which will be useful for further sampling.
>> To tell the truth I couldn't get summary.dat by "perl distance.pl" 
>> command.as I'm not good in programming I couldn't understand what happened 
>> there?!
>
> Run gmx distance manually. It's probably returning some error, so the script 
> fails. I've heard this reported a number of times and no one's ever told me 
> what the solution is, so unfortunately there's nothing I can do to fix it.
>
>> How did you know for example:
>> 50>>>0.6 nm
>> 100>>>0.8 nm
>
> This is what gmx distance computes.
>
>> I need deltaz=0.05nm
>
> Then you will need to save frames very frequently. This is a very narrow dz, 
> and may be overkill depending on what the system is.
>
>> Please help me, i don't know where should i find these informations and 
>> modify them.
>>
>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far 
>> from it (and rvdw and coulomb=1.5 and
>
> What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs 
> used by any given force field, as you will get unexpected (or invalid) 
> results...
>
>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to 
>> wall(4nm far from slab) except slab.
>> What is my mistake?!
>
> You'll have to provide an .mdp file and a complete description of your 
> system, how you constructed it, and what your objectives are. Images would 
> help.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
-- 
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/24/17 9:14 AM, Rose wrote:

Hello

I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial 
with MR Lemkul) But I don't know how should I implement deltaZ and how choose 
different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as 
I'm not good in programming I couldn't understand what happened there?!


Run gmx distance manually. It's probably returning some error, so the 
script fails. I've heard this reported a number of times and no one's 
ever told me what the solution is, so unfortunately there's nothing I 
can do to fix it.



How did you know for example:
50>>>0.6 nm
100>>>0.8 nm


This is what gmx distance computes.


I need deltaz=0.05nm


Then you will need to save frames very frequently. This is a very narrow 
dz, and may be overkill depending on what the system is.



Please help me, i don't know where should i find these informations and modify 
them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from 
it (and rvdw and coulomb=1.5 and


What force field uses such a cutoff? Don't make ad hoc changes to the 
cutoffs used by any given force field, as you will get unexpected (or 
invalid) results...



rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to 
wall(4nm far from slab) except slab.
What is my mistake?!


You'll have to provide an .mdp file and a complete description of your 
system, how you constructed it, and what your objectives are. Images 
would help.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Umbrella sampling: issue with COM distance far from initial value

[Wes Barnett]

On Tue, Oct 17, 2017 at 8:05 AM, Giuseppe Léonardo Licari <
giuseppe.lic...@unige.ch> wrote:

> Dear all,
>
> I have troubles with umbrella sampling. During the umbrella sampling
> simulation the COM distance between the two solutes is going too far from
> the set initial value. I tried to increase a lot the force constant of the
> harmonic potential. I also tried to change "umbrella" to "contraint", with
> no success. How can I fix the COM distance between the two solutes? It
> seems that increasing the force constant does not work. Am I making some
> mistake in the input? I have Gromacs v. 5.1.2 and here you can find the
> files of a test simulation:
>
> https://www.dropbox.com/s/cl7au3twx8d6iip/test.zip?dl=0
>
> As you see from the trajectory the two solutes go very far from the
> initial COM distance. Does somebody have an idea about this?
>
> Thanks for the help and have a nice day.
> Regards,
> Licari
> Giuseppe
>

I viewed the trajectory, but I can't see anything wrong. The two solutes
seem to maintain a COM to COM distance that they started with. Note you are
only doing the pull code on the z-vector so they are allowed to move as far
as they want in the x and y directions from each other. Also your are using
direction-periodic, which is probably not what you want.

Use a bigger box, and use the distance method, or if you want to just do it
along the z-vector (with direction, not direction-periodic) you will
probably have to use a flat-bottom restraint to keep your solutes along the
z-axis.

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 9/2/17 10:28 AM, sp...@iacs.res.in wrote:

  Hi all
I am trying to do umbrella sampling of protein unfolding with radius of
gyration as reaction coordinate using gromacs-2016.3 patched with
plumed-2.3.2. I want to calculate free energy for the system. I am using
the following command

gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat  free.dat



None of this is valid syntax.


It shows an error
  Fatal error:
  Give either pullx (-ix) OR pullf (-if) data. Not both.

But I am using radius of gyration as variable.Why I need to give pullx ?
Please anyone help.



gmx wham assumes you're using the GROMACS pull code, therefore relying entirely 
on GROMACS input and output files.  If you're doing something else, you're going 
to need to use another program (e.g. Alan Grossfield's WHAM program or whatever 
else the PLUMED community suggests).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 5:29 PM, Ben Tam wrote:

Hi Justin,

Thanks for answering. I have tried sending the histogram however it is too big 
of a file. But the histogram shows a lot of overlapping and multiple peaks. All 
of the value in profile.xvg  showing nan. What can that mean?




Most likely a sampling problem.  But as I cannot see your histograms, I can't 
guess any further at specifically what's going on.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 1:38 PM, Ben Tam wrote:

Hi Justin,


I am trying to get an energy profile when water molecules go through the porous 
cage. I am restraint it to z direction because I would like to see the energy 
that require to jump from one cage to another. I set up the simulation so that 
the structure is repeated at z direction which this will give me more sample 
slice for starting configuration. Sorry I am still new to the umbrella sampling.



OK, I see what you're doing now.  That should be fine, but without seeing the 
histograms it's impossible to know how well things are working.  If you're 
getting NaN somewhere, that means a gap in the sampling.


-Justin



Best regards,


Ben





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling



On 7/11/17 12:53 PM, Ben Tam wrote:

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework 
that I am working on which is a porous material. With the k value larger than 
100, the histogram become multiple sharp single peak.

Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".




I'm really confused about your setup.  From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z.  What is
the geometry of your system?  Don't follow my tutorial too closely, it's not
appropriate for most cases...

-Justin



Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias de 
Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:


Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?

Best regards,

Ben


--
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==

Re: [gmx-users] umbrella sampling

[Ben Tam]

Hi Justin,


I am trying to get an energy profile when water molecules go through the porous 
cage. I am restraint it to z direction because I would like to see the energy 
that require to jump from one cage to another. I set up the simulation so that 
the structure is repeated at z direction which this will give me more sample 
slice for starting configuration. Sorry I am still new to the umbrella sampling.


Best regards,


Ben





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling



On 7/11/17 12:53 PM, Ben Tam wrote:
> Hi Andre,
>
>
> Thanks for your answer. Actually I should clarify it is 
> metal-organic-framework that I am working on which is a porous material. With 
> the k value larger than 100, the histogram become multiple sharp single peak.
Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".
>

I'm really confused about your setup.  From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z.  What is
the geometry of your system?  Don't follow my tutorial too closely, it's not
appropriate for most cases...

-Justin

>
> Best regards,
>
>
> Ben
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias 
> de Moura <mo...@ufscar.br>
> Sent: Tuesday, July 11, 2017 17:44
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] umbrella sampling
>
> I never did it myself, but generally speaking you don' t expect that there'
> s a lot of room inside a crystal for any molecule to diffuse there,
> especially when it comes to cross something like a crystallographic plane,
> meaning that huge energy barriers should be there, leading to NaN and other
> weird numerical issues.
>
> in principle, larger force constants might help you to sample high energy
> barrier, but it will be most likely a trial and error procedure until you
> fine-tune the forces along the profile.
>
> best
>
> Andre
>
> On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:
>
>> Dear All,
>>
>> I am doing umbrella sampling for a water molecules moving inside a crystal
>> structure, however I am running into a problem on the output file with
>> profile.xvg all value showing “nan”. This error has occurred when I reduce
>> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
>> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
>> code I used is the following:
>>
>> ;Pull code
>> pull = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = MOL
>> pull_group2_name = SOL
>> pull_coord1_type = umbrella ; harmonic biasing force
>> pull_coord1_geometry = distance ; simple distance increase
>> ;pull_coord1_vec = 0 0 1
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes ; define initial COM distance > 0
>>
>> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
>> have tried increasing the k value to 50 and 100 with the same results.
>>
>> The histogram shows many overlap, however when I use k value 100, it is
>> only giving me individual single peak. Therefore can someone enlighten on
>> what is going on?
>>
>> Best regards,
>>
>> Ben
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support

> Support - Gromacs<http://www.gromacs.org/Support>

> www.gromacs.org<http://www.gromacs.org>
> When posting a request for assistance to the Mailing Lists, be sure to. cite 
> your GROMACS version number (and if it's not the most recent, try installing 
> that first!),
>
>
>
>> /Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 12:53 PM, Ben Tam wrote:

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework that I am working on which is a porous material. With the k value larger than 100, the histogram become multiple sharp single peak. 
Furthermore when I look at individual 0.1nm slides, it runs completely fine 
without obvious anomaly. Therefore I am really confused why the profile.xvg 
become infinite or "nan".




I'm really confused about your setup.  From what it sounds like, your windows 
are too narrow to get good sampling, perhaps the force constant is too strong, 
and I'm really not sure why you're only applying a restraint along z.  What is 
the geometry of your system?  Don't follow my tutorial too closely, it's not 
appropriate for most cases...


-Justin



Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias de 
Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:


Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?

Best regards,

Ben


--
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* Please search the archive at http://www.gromacs.org/Support

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--
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] umbrella sampling

[Ben Tam]

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework 
that I am working on which is a porous material. With the k value larger than 
100, the histogram become multiple sharp single peak. Furthermore when I look 
at individual 0.1nm slides, it runs completely fine without obvious anomaly. 
Therefore I am really confused why the profile.xvg become infinite or "nan".


Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias 
de Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:

> Dear All,
>
> I am doing umbrella sampling for a water molecules moving inside a crystal
> structure, however I am running into a problem on the output file with
> profile.xvg all value showing “nan”. This error has occurred when I reduce
> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
> code I used is the following:
>
> ;Pull code
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = MOL
> pull_group2_name = SOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> ;pull_coord1_vec = 0 0 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
> have tried increasing the k value to 50 and 100 with the same results.
>
> The histogram shows many overlap, however when I use k value 100, it is
> only giving me individual single peak. Therefore can someone enlighten on
> what is going on?
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
Support - Gromacs<http://www.gromacs.org/Support>
www.gromacs.org
When posting a request for assistance to the Mailing Lists, be sure to. cite 
your GROMACS version number (and if it's not the most recent, try installing 
that first!),



> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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www.gromacs.org
The three mailing lists (see the menu items on the left) have slightly 
different purposes, and you might not be interested in subscribing to all of 
them:



>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>



--
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
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...<https://maillist.sys.kth.se/m

Re: [gmx-users] umbrella sampling

[André Farias de Moura]

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:

> Dear All,
>
> I am doing umbrella sampling for a water molecules moving inside a crystal
> structure, however I am running into a problem on the output file with
> profile.xvg all value showing “nan”. This error has occurred when I reduce
> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
> code I used is the following:
>
> ;Pull code
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = MOL
> pull_group2_name = SOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> ;pull_coord1_vec = 0 0 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
> have tried increasing the k value to 50 and 100 with the same results.
>
> The histogram shows many overlap, however when I use k value 100, it is
> only giving me individual single peak. Therefore can someone enlighten on
> what is going on?
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 6/14/17 10:52 PM, Kingsley Theras Primus Dass . wrote:

Hii
  I am trying out the umbrella sampling tutorial. I finished generating a
series of coordinate file , but when i run the perl script the
summary_distance.dat doesnt generate the COM distance value 
What would be the possible reason for this ?



People keep reporting this and I never find out why, but the advice is the same 
- abandon the script and try one of the calls to gmx distance yourself.  It will 
print an error that you can diagnose.  Probably your index file isn't set up 
correctly.  If you do work it out, please report back so I know if there's 
actually something wrong (the script itself is quite trivial so I know that's 
not the problem, but maybe something about the call to gmx distance is).


-Justin

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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
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Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Alex]

>
>
>>
> A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.


The pull vector is exactly as set by you to N N Y, maybe the code
multiplies the vector components by the corresponding pull rates and then
checks the resulting velocity vector, I don't know, but the error is there
with 5.1.*,. No error when using GMX 5.0.4 i have on a local machine, btw.
I'll get back to you on the exact input file and the GMX version.


>
>>>

 Old GROMACS versions had a "position" geometry that was the go-to for
>>> membrane/slab/layered systems and worked quite nicely, but that's gone
>>> now,
>>> replaced by other options that I've never used.
>>>
>>
>>
>> How old? I have 5.0.4 on another machine here...
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/2/17 6:40 PM, Alex wrote:


I find that surprising.  Please provide the full, exact error and your

pull settings.  All of the geometries should work with zero or non-zero
pull rates. But I admit, it has been many years since I used GROMACS with
the pull code.




Simply take your pull code from the tutorial and replace 'distance' with
'direction-periodic' or 'cylinder' (along with some r0/r1). The error is
that the pull vector cannot be (0 0 0), do not remember the exact text.


A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.


Setting the pull rate to something like 1e-12 results in the same error.
Our cluster is down for maintenance until Monday, will give you the exact
excerpt, if needed.



If you want to troubleshoot further, yes.

-Justin








Old GROMACS versions had a "position" geometry that was the go-to for
membrane/slab/layered systems and worked quite nicely, but that's gone now,
replaced by other options that I've never used.



How old? I have 5.0.4 on another machine here...



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Umbrella sampling and PMF calculations

[Alex]

>
> I find that surprising.  Please provide the full, exact error and your
>> pull settings.  All of the geometries should work with zero or non-zero
>> pull rates. But I admit, it has been many years since I used GROMACS with
>> the pull code.
>>
>
Simply take your pull code from the tutorial and replace 'distance' with
'direction-periodic' or 'cylinder' (along with some r0/r1). The error is
that the pull vector cannot be (0 0 0), do not remember the exact text.
Setting the pull rate to something like 1e-12 results in the same error.
Our cluster is down for maintenance until Monday, will give you the exact
excerpt, if needed.

>
>
>>
>>
> Old GROMACS versions had a "position" geometry that was the go-to for
> membrane/slab/layered systems and worked quite nicely, but that's gone now,
> replaced by other options that I've never used.


How old? I have 5.0.4 on another machine here...
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/2/17 4:17 PM, Alex wrote:

So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my


I find that surprising.  Please provide the full, exact error and your pull 
settings.  All of the geometries should work with zero or non-zero pull rates. 
But I admit, it has been many years since I used GROMACS with the pull code.



particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup? I'd understand if the entire membrane was reactive, but it
isn't. Also, the obtained free energy value is very close to what one gets
by simply integrating the pullf data wrt pull coordinate, which makes
perfect sense. Any comments/suggestions?



You might get some windows that conveniently work with "simpler" settings but I 
still think you need to do what I said before.  Old GROMACS versions had a 
"position" geometry that was the go-to for membrane/slab/layered systems and 
worked quite nicely, but that's gone now, replaced by other options that I've 
never used.


-Justin


Thanks,

Alex

On Fri, Jun 2, 2017 at 11:26 AM, Alex  wrote:







Yes, because if your ion diffuses laterally (or whatever constitutes your
"hole"), then you're not sampling what you think you're sampling.  That's
what the cylinder geometry is for.  You have a system capable of
significant lateral movement, so if you fail to apply a bias that acts in
the x-y plane, your results are very quickly going to become garbage.

-Justin

Of course. I actually realized that you used COM distance and not e.g.

direction-periodic (which won't accept zero pulling rates anyway) only
after I asked.
Specifying somewhat awkward structures like disks as references could be
avoided by simply allowing a component of the COM distance vector and not
the entire vector) to be used. Anyway, doesn't really matter.

Thanks,

Alex



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Alex]

So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup? I'd understand if the entire membrane was reactive, but it
isn't. Also, the obtained free energy value is very close to what one gets
by simply integrating the pullf data wrt pull coordinate, which makes
perfect sense. Any comments/suggestions?

Thanks,

Alex

On Fri, Jun 2, 2017 at 11:26 AM, Alex  wrote:

>
>
>>>
>> Yes, because if your ion diffuses laterally (or whatever constitutes your
>> "hole"), then you're not sampling what you think you're sampling.  That's
>> what the cylinder geometry is for.  You have a system capable of
>> significant lateral movement, so if you fail to apply a bias that acts in
>> the x-y plane, your results are very quickly going to become garbage.
>>
>> -Justin
>>
>> Of course. I actually realized that you used COM distance and not e.g.
> direction-periodic (which won't accept zero pulling rates anyway) only
> after I asked.
> Specifying somewhat awkward structures like disks as references could be
> avoided by simply allowing a component of the COM distance vector and not
> the entire vector) to be used. Anyway, doesn't really matter.
>
> Thanks,
>
> Alex
>
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