[gmx-users] Problem on pbc atom

[Mahsa Rezaei]

Dear gromacs users,
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
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.


when I execute this command,I got warning:

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


WARNING 1 [file md_pull.mdp]:
  Pull group 1 has atoms at a distance larger than 0.9 times half the box
  size from the PBC atom (27119). If atoms are or will more beyond half the
  box size from the PBC atom, the COM will be ill defined.

Pull group  natoms  pbc atom  distance at start  reference at t=0
   1 54231 27120
   2 4 2  -3.769 nm -3.769 nm
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 1238 Mb of data

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

What should I do?
I would be very appreciated for your such kind helps.

My mdp file  :

integrator  = md
dt  = 0.002
nsteps  = 29 ; 580 ps
; Output parameters
nstlog  = 1000
nstxout = 500   ; every 1 ps
nstvout = 500
nstfout = 500
nstxtcout   = 500; every 1 ps
nstcalcenergy   = 500
nstenergy   = 500

cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
;
tcoupl  = Nose-Hoover
tc_grps = PROT  MEMB_LIG  SOL_ION
tau_t   = 1.01.01.0
ref_t   = 303.15 303.15 303.15
;
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = PROT MEMB_LIG SOL_ION
;
refcoord_scaling= com

; Pull code
pull   = yes
pull_ncoords   = 1 ; only one reaction coordinate
pull_ngroups   = 2
pull_group1_name   = BILAYER
pull_group2_name   = LIG
pull_coord1_type   = umbrella  ; harmonic potential
pull_coord1_geometry   = direction
pull_coord1_vec= 0.0 0.0 1.0
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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[gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear gromacs users,

Sorry for repeating my question.

I didn't receive any email so I couldn't reply and I missed

them.

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

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[gmx-users] (no subject)

[Mahsa Rezaei]

Dear gromacs users,

Sorry for repeating my question.

I didn't receive any email so I couldn't reply and I missed

 them.

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

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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




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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
>
>
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>  09/24/19,
> 01:19:54 PM
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[gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

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 .

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
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
-
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]
*>* <
*>* 
https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
<https://mailtrack.io/?utm_source=gmail_medium=signature_campaign=signaturevirality5;

[gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

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] Some suggestions about the gmx current tool

[Mahsa]

Hi Mark,

Thank you for your reply!
I opened a new issue with this information in the link you mentioned.

Best regards,
Mahsa

On Wed, Jun 12, 2019 at 10:26 PM Mark Abraham 
wrote:

> Hi Mahsa,
>
> Thanks very much for your feedback. Those look like useful changes to the
> code. Can you please open an issue at https://redmine.gromacs.org with
> that
> information? You'll also be able to attach files, unlike on this list :-)
>
> Mark
>
> On Wed., 12 Jun. 2019, 15:21 Mahsa,  wrote:
>
> > Hi again,
> >
> > Something went wrong with the equations which I tried to show.
> >
> > So for the first equation please see eq. 9 in this paper:
> >
> > https://aip.scitation.org/doi/10.1063/1.2868752
> >
> > and the second missing formula is:
> >
> > 1 / 6*V*K_B*T = 7.20677e-12
> >
> > Best regards,
> > Mahsa
> >
> >
> > On Wed, Jun 12, 2019 at 3:12 PM Mahsa  wrote:
> >
> > > Hi gmx-users,
> > >
> > > I use gmx current tool to calculate static conductivity by version
> 2018:
> > >
> > > gmx current -f md.xtc -o -dsp -md -mj -temp 423 -nojump -n index.ndx -s
> > > topol.tpr
> > >
> > > Indeed the tool is useful, but I think some parts in the output are
> > > confusing and need to be improved.
> > > I think the generated dsp.xvg file which reports the MSD of
> translational
> > > dipole moments vs time has the wrong unit in the plot. The unit should
> be
> > > (S/m) ps according to this equation:
> > > [image: Screen Shot 2019-06-12 at 14.35.45.png]
> > > and the pre-factor fit reported in the output of dsp.xvg in my case is:
> > >
> > > [image: Screen Shot 2019-06-12 at 14.37.37.png]
> > > but [(1.6 * 10^-19)^2 * (10^-18)] / [6*V*K_B*T] is equal to 7.20677e-12
> > > considering the conversion of MSD of dipole moments from (enm)^2 to
> > (em)^2
> > > so it would be really helpful to add a hint in the documentation or the
> > > code about that.
> > > Finally, as far as I understood the reported sigma value in the output
> of
> > > dsp.xvg should be multiplied by 10^-12 manually.
> > > It took sometime for me to understand what is going on in the output
> :-)
> > > Please correct me if I'm wrong or missed something in these comments.
> > >
> > > Best regards,
> > > Mahsa
> > >
> > >
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Some suggestions about the gmx current tool

[Mahsa]

Hi again,

Something went wrong with the equations which I tried to show.

So for the first equation please see eq. 9 in this paper:

https://aip.scitation.org/doi/10.1063/1.2868752

and the second missing formula is:

1 / 6*V*K_B*T = 7.20677e-12

Best regards,
Mahsa


On Wed, Jun 12, 2019 at 3:12 PM Mahsa  wrote:

> Hi gmx-users,
>
> I use gmx current tool to calculate static conductivity by version 2018:
>
> gmx current -f md.xtc -o -dsp -md -mj -temp 423 -nojump -n index.ndx -s
> topol.tpr
>
> Indeed the tool is useful, but I think some parts in the output are
> confusing and need to be improved.
> I think the generated dsp.xvg file which reports the MSD of translational
> dipole moments vs time has the wrong unit in the plot. The unit should be
> (S/m) ps according to this equation:
> [image: Screen Shot 2019-06-12 at 14.35.45.png]
> and the pre-factor fit reported in the output of dsp.xvg in my case is:
>
> [image: Screen Shot 2019-06-12 at 14.37.37.png]
> but [(1.6 * 10^-19)^2 * (10^-18)] / [6*V*K_B*T] is equal to 7.20677e-12
> considering the conversion of MSD of dipole moments from (enm)^2 to (em)^2
> so it would be really helpful to add a hint in the documentation or the
> code about that.
> Finally, as far as I understood the reported sigma value in the output of
> dsp.xvg should be multiplied by 10^-12 manually.
> It took sometime for me to understand what is going on in the output :-)
> Please correct me if I'm wrong or missed something in these comments.
>
> Best regards,
> Mahsa
>
>
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[gmx-users] Some suggestions about the gmx current tool

[Mahsa]

Hi gmx-users,

I use gmx current tool to calculate static conductivity by version 2018:

gmx current -f md.xtc -o -dsp -md -mj -temp 423 -nojump -n index.ndx -s
topol.tpr

Indeed the tool is useful, but I think some parts in the output are
confusing and need to be improved.
I think the generated dsp.xvg file which reports the MSD of translational
dipole moments vs time has the wrong unit in the plot. The unit should be
(S/m) ps according to this equation:
[image: Screen Shot 2019-06-12 at 14.35.45.png]
and the pre-factor fit reported in the output of dsp.xvg in my case is:

[image: Screen Shot 2019-06-12 at 14.37.37.png]
but [(1.6 * 10^-19)^2 * (10^-18)] / [6*V*K_B*T] is equal to 7.20677e-12
considering the conversion of MSD of dipole moments from (enm)^2 to (em)^2
so it would be really helpful to add a hint in the documentation or the
code about that.
Finally, as far as I understood the reported sigma value in the output of
dsp.xvg should be multiplied by 10^-12 manually.
It took sometime for me to understand what is going on in the output :-)
Please correct me if I'm wrong or missed something in these comments.

Best regards,
Mahsa
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[gmx-users] (no subject)

[Mahsa Rezaei]

mahs.rez...@mail.sbu.ac.ir
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[gmx-users] Contact autocorrelation function in Gromacs

[Mahsa]

Dear all,

I want to calculate the contact duration of ions with special atoms in
polymer chains within 3 Å of the ion.
I found gmx hbond as a good option for this analysis, but I have some
questions regarding this calculation. By the way, the version of gromacs is
2018.3.
1.  I used the following command:
gmx  hbond -s topol.tpr -f md.xtc -n index_contact.ndx -contact -r 0.3 -num
contact.xvg -g contact.log -ac contact_ac.xvg
in the gromacs manual it is not clear whether r or r2 should be used for
this analysis. I tried this as well:
gmx  hbond -s topol.tpr -f md.xtc -n index_contact.ndx -contact -r2 0.3
-num contact.xvg -g contact.log -ac contact_ac.xvg
The final results were little bit different from the first one. Which one
is correct -r or -r2?
2. At the end of this calculation, I get the following warning:
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001

I used the trajectory of 500 ns simulation time but still get this warning.
I also tried trajectory with saving every frame but still get the warning.
How can I solve this?
3. The tail of ACF goes to negative values, I found this link for the
similar question:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/062181.html
Does this means that I should consider the second column of y values in the
contac_ac.xvg file instead of the first one?

Best regards,
Mahsa
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Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Hi,

When I use the tool, gmx analyze -dist, on the generated file from gmx
mindist for the number of contact, I can get the probability of number of
contacts. So I think if an appropriate index file and cut off distance are
defined by using this approach, I can get the probability of the first
shell coordination number for specific groups during the simulation time.
Is this correct? because the coordination number from gmx rdf gives the
average number of particles within a distance r.

Best regards,
Mahsa

On Fri, Mar 1, 2019 at 12:11 PM Mahsa  wrote:

> Hi Mark,
>
> Thank you for your reply! Actually, I should clarify my last post because
> it seems that I repeated my question :-)
> When I use the tool that Justin suggested, gmx analyze -dist, on the
> generated file from gmx mindist for the number of contact, I can get the
> probability of number of contacts. So I think if an appropriate index file
> and cut off distance are defined by using this approach, I can get the
> probability of the first shell coordination number for specific groups
> during the simulation time. Is this correct? because the coordination
> number from gmx rdf gives the average number of particles within a distance
> r.
>
> Best regards,
> Mahsa
>
> On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Which GROMACS tools documentation did you check to see whether it can be
>> done already? :-) I don't know the answer, but that's where to start!
>>
>> Mark
>>
>> On Thu., 28 Feb. 2019, 10:43 Mahsa,  wrote:
>>
>> > Thank you very much for your comments!
>> >
>> > How would it be possible to get probability vs. number of contacts or
>> > probability vs coordination number averaged across the simulations? Can
>> it
>> > be done directly with Gromacs tools or I need some scripts for that?
>> >
>> > Best regards,
>> > Mahsa
>> >
>> > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:
>> >
>> > >
>> > >
>> > > On 2/28/19 8:59 AM, Mahsa wrote:
>> > > > Hi Justin,
>> > > >
>> > > > Could you please comment on my questions in the previous post?
>> > > >
>> > > > Best regards,
>> > > > Mahsa
>> > > >
>> > > > -- Forwarded message -
>> > > > From: Mahsa 
>> > > > Date: Sun, Feb 17, 2019 at 2:36 PM
>> > > > Subject: Re: [gmx-users] Probability of number of atomic contacts
>> > > > To: 
>> > > >
>> > > >
>> > > > Thank you very much, Justin!
>> > > >
>> > > > I tried this command:
>> > > >
>> > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
>> > > >
>> > > >
>> > > > and I got a histogram. Now the number of contacts between the ion
>> and
>> > the
>> > > > polymer is between 160-180. I just want to be sure if I am doing
>> this
>> > > > analysis correct. When I use gmx mindist, from the index file I
>> choose
>> > a
>> > > > group of the ion (including 46 ions) and then the polymer group (all
>> > > > polymer chains in the box).  I think maybe instead of choosing all
>> > ions,
>> > > I
>> > > > should only select one of them and get the number of contact with
>> the
>> > > > polymers but then since I have 46 of this ion in the simulation box,
>> > can
>> > > it
>> > > > be a good representative of the whole system? If not, what else can
>> I
>> > do
>> > > in
>> > > > this case?
>> > >
>> > > I don't see any point in doing per-ion analysis. You already have the
>> > > answer you want with respect to contacts between the two species.
>> > > Choosing one ion isn't necessarily going to be representative, either.
>> > >
>> > > > Besides, it is mentioned in the Gromacs manual, that if we use the
>> > > > -group option
>> > > > a contact of an atom in another group with multiple atoms in the
>> first
>> > > > group is counted as one contact instead of as multiple contacts. I
>> want
>> > > to
>> > > > count all contact with a polymer chain as 1 contact and check the
>> > number
>> > > of
>> > > > contacts with different polymer chains so by using -group and having
>> > the
>> > > > ion as the fi

Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Hi Mark,

Thank you for your reply! Actually, I should clarify my last post because
it seems that I repeated my question :-)
When I use the tool that Justin suggested, gmx analyze -dist, on the
generated file from gmx mindist for the number of contact, I can get the
probability of number of contacts. So I think if an appropriate index file
and cut off distance are defined by using this approach, I can get the
probability of the first shell coordination number for specific groups
during the simulation time. Is this correct? because the coordination
number from gmx rdf gives the average number of particles within a distance
r.

Best regards,
Mahsa

On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham 
wrote:

> Hi,
>
> Which GROMACS tools documentation did you check to see whether it can be
> done already? :-) I don't know the answer, but that's where to start!
>
> Mark
>
> On Thu., 28 Feb. 2019, 10:43 Mahsa,  wrote:
>
> > Thank you very much for your comments!
> >
> > How would it be possible to get probability vs. number of contacts or
> > probability vs coordination number averaged across the simulations? Can
> it
> > be done directly with Gromacs tools or I need some scripts for that?
> >
> > Best regards,
> > Mahsa
> >
> > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 2/28/19 8:59 AM, Mahsa wrote:
> > > > Hi Justin,
> > > >
> > > > Could you please comment on my questions in the previous post?
> > > >
> > > > Best regards,
> > > > Mahsa
> > > >
> > > > -- Forwarded message -
> > > > From: Mahsa 
> > > > Date: Sun, Feb 17, 2019 at 2:36 PM
> > > > Subject: Re: [gmx-users] Probability of number of atomic contacts
> > > > To: 
> > > >
> > > >
> > > > Thank you very much, Justin!
> > > >
> > > > I tried this command:
> > > >
> > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
> > > >
> > > >
> > > > and I got a histogram. Now the number of contacts between the ion and
> > the
> > > > polymer is between 160-180. I just want to be sure if I am doing this
> > > > analysis correct. When I use gmx mindist, from the index file I
> choose
> > a
> > > > group of the ion (including 46 ions) and then the polymer group (all
> > > > polymer chains in the box).  I think maybe instead of choosing all
> > ions,
> > > I
> > > > should only select one of them and get the number of contact with the
> > > > polymers but then since I have 46 of this ion in the simulation box,
> > can
> > > it
> > > > be a good representative of the whole system? If not, what else can I
> > do
> > > in
> > > > this case?
> > >
> > > I don't see any point in doing per-ion analysis. You already have the
> > > answer you want with respect to contacts between the two species.
> > > Choosing one ion isn't necessarily going to be representative, either.
> > >
> > > > Besides, it is mentioned in the Gromacs manual, that if we use the
> > > > -group option
> > > > a contact of an atom in another group with multiple atoms in the
> first
> > > > group is counted as one contact instead of as multiple contacts. I
> want
> > > to
> > > > count all contact with a polymer chain as 1 contact and check the
> > number
> > > of
> > > > contacts with different polymer chains so by using -group and having
> > the
> > > > ion as the first group and polymer as the second group from the index
> > > file,
> > > > can I get this?
> > >
> > > This option is primarily used to avoid over-counting, e.g. the
> > > interaction between an ion and carboxylate oxygens will not be counted
> > > as two contact if each ion-oxygen distance satisfies the criterion;
> it's
> > > just one.
> > >
> > > > The last question, can I do the same approach to get the distribution
> > of
> > > > coordination number for the first coordination shell of ions and
> > special
> > > > atoms of the polymers?
> > >
> > > You can calculate coordination number by integrating an RDF.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> >

Re: [gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Thank you very much for your comments!

How would it be possible to get probability vs. number of contacts or
probability vs coordination number averaged across the simulations? Can it
be done directly with Gromacs tools or I need some scripts for that?

Best regards,
Mahsa

On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul  wrote:

>
>
> On 2/28/19 8:59 AM, Mahsa wrote:
> > Hi Justin,
> >
> > Could you please comment on my questions in the previous post?
> >
> > Best regards,
> > Mahsa
> >
> > -- Forwarded message -
> > From: Mahsa 
> > Date: Sun, Feb 17, 2019 at 2:36 PM
> > Subject: Re: [gmx-users] Probability of number of atomic contacts
> > To: 
> >
> >
> > Thank you very much, Justin!
> >
> > I tried this command:
> >
> > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg
> >
> >
> > and I got a histogram. Now the number of contacts between the ion and the
> > polymer is between 160-180. I just want to be sure if I am doing this
> > analysis correct. When I use gmx mindist, from the index file I choose a
> > group of the ion (including 46 ions) and then the polymer group (all
> > polymer chains in the box).  I think maybe instead of choosing all ions,
> I
> > should only select one of them and get the number of contact with the
> > polymers but then since I have 46 of this ion in the simulation box, can
> it
> > be a good representative of the whole system? If not, what else can I do
> in
> > this case?
>
> I don't see any point in doing per-ion analysis. You already have the
> answer you want with respect to contacts between the two species.
> Choosing one ion isn't necessarily going to be representative, either.
>
> > Besides, it is mentioned in the Gromacs manual, that if we use the
> > -group option
> > a contact of an atom in another group with multiple atoms in the first
> > group is counted as one contact instead of as multiple contacts. I want
> to
> > count all contact with a polymer chain as 1 contact and check the number
> of
> > contacts with different polymer chains so by using -group and having the
> > ion as the first group and polymer as the second group from the index
> file,
> > can I get this?
>
> This option is primarily used to avoid over-counting, e.g. the
> interaction between an ion and carboxylate oxygens will not be counted
> as two contact if each ion-oxygen distance satisfies the criterion; it's
> just one.
>
> > The last question, can I do the same approach to get the distribution of
> > coordination number for the first coordination shell of ions and special
> > atoms of the polymers?
>
> You can calculate coordination number by integrating an RDF.
>
> -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
>
> ==
>
> --
> 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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[gmx-users] Fwd: Probability of number of atomic contacts

[Mahsa]

Hi Justin,

Could you please comment on my questions in the previous post?

Best regards,
Mahsa

-- Forwarded message -
From: Mahsa 
Date: Sun, Feb 17, 2019 at 2:36 PM
Subject: Re: [gmx-users] Probability of number of atomic contacts
To: 


Thank you very much, Justin!

I tried this command:

gmx_seq analyze -f numcont.xvg -dist num_dist.xvg


and I got a histogram. Now the number of contacts between the ion and the
polymer is between 160-180. I just want to be sure if I am doing this
analysis correct. When I use gmx mindist, from the index file I choose a
group of the ion (including 46 ions) and then the polymer group (all
polymer chains in the box).  I think maybe instead of choosing all ions, I
should only select one of them and get the number of contact with the
polymers but then since I have 46 of this ion in the simulation box, can it
be a good representative of the whole system? If not, what else can I do in
this case?

Besides, it is mentioned in the Gromacs manual, that if we use the
-group option
a contact of an atom in another group with multiple atoms in the first
group is counted as one contact instead of as multiple contacts. I want to
count all contact with a polymer chain as 1 contact and check the number of
contacts with different polymer chains so by using -group and having the
ion as the first group and polymer as the second group from the index file,
can I get this?

The last question, can I do the same approach to get the distribution of
coordination number for the first coordination shell of ions and special
atoms of the polymers?

Best regards,
Mahsa

On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul  wrote:

>
>
> On 2/17/19 7:21 AM, Mahsa wrote:
> > Dear Gromacs users,
> >
> > I want to get histograms of the number of polymer-ion contacts average
> > across the simulation. For this I used,
> >
> > gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od
> mindist.xvg
> > -on numcont.xvg -or mindistres.xvg -group
> >
> > and from the index file, I chose the ion first and then the polymer
> group.
> > The generated file numcont.xvg which is more related to what I am looking
> > for, gives number of contacts vs time. How can I get the information
> which
> > I look for from this analysis?
>
> Post-process with gmx analyze -dist
>
> -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
>
> ==
>
> --
> 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] Probability of number of atomic contacts

[Mahsa]

Thank you very much, Justin!

I tried this command:

gmx_seq analyze -f numcont.xvg -dist num_dist.xvg


and I got a histogram. Now the number of contacts between the ion and the
polymer is between 160-180. I just want to be sure if I am doing this
analysis correct. When I use gmx mindist, from the index file I choose a
group of the ion (including 46 ions) and then the polymer group (all
polymer chains in the box).  I think maybe instead of choosing all ions, I
should only select one of them and get the number of contact with the
polymers but then since I have 46 of this ion in the simulation box, can it
be a good representative of the whole system? If not, what else can I do in
this case?

Besides, it is mentioned in the Gromacs manual, that if we use the
-group option
a contact of an atom in another group with multiple atoms in the first
group is counted as one contact instead of as multiple contacts. I want to
count all contact with a polymer chain as 1 contact and check the number of
contacts with different polymer chains so by using -group and having the
ion as the first group and polymer as the second group from the index file,
can I get this?

The last question, can I do the same approach to get the distribution of
coordination number for the first coordination shell of ions and special
atoms of the polymers?

Best regards,
Mahsa

On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul  wrote:

>
>
> On 2/17/19 7:21 AM, Mahsa wrote:
> > Dear Gromacs users,
> >
> > I want to get histograms of the number of polymer-ion contacts average
> > across the simulation. For this I used,
> >
> > gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od
> mindist.xvg
> > -on numcont.xvg -or mindistres.xvg -group
> >
> > and from the index file, I chose the ion first and then the polymer
> group.
> > The generated file numcont.xvg which is more related to what I am looking
> > for, gives number of contacts vs time. How can I get the information
> which
> > I look for from this analysis?
>
> Post-process with gmx analyze -dist
>
> -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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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[gmx-users] Probability of number of atomic contacts

[Mahsa]

Dear Gromacs users,

I want to get histograms of the number of polymer-ion contacts average
across the simulation. For this I used,

gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od mindist.xvg
-on numcont.xvg -or mindistres.xvg -group

and from the index file, I chose the ion first and then the polymer group.
The generated file numcont.xvg which is more related to what I am looking
for, gives number of contacts vs time. How can I get the information which
I look for from this analysis?

Best regards,
Mahsa
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Thank you for your reply!

Best regards,
Mahsa

On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham 
wrote:

> Hi,
>
> You need a composite selection, eg of an atomtype and residue type or
> molecule type. Make a selection of the atomtype and another of whatever
> seems suitable, and combine them.
>
> Mark
>
> On Sat, Aug 11, 2018, 13:53 Mahsa  wrote:
>
> > Hi Mark,
> >
> > Thank you for your reply!
> >
> > I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> > based on the atom types which worked very well. The only problem is I
> need
> > to also compute the RDF for the O of the side chain with the same atom
> type
> > as the ester O in the polymer. Then with this approach I get both O types
> > in a group while I should have them separately. Could you help me with
> this
> > problem? I don't know how to specify this one for the RDF calculations.
> >
> > Best regards,
> > Mahsa
> >
> >
> >
> >
> >
> > On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > Making a selection with a tool like gmx select or gmx make_ndx is a
> good
> > > way to select e.g. by atomtype.
> > >
> > > Mark
> > >
> > > On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
> > >
> > > > Hello,
> > > >
> > > > I would like to calculate the RDF between some ions and oxygen atoms
> > of a
> > > > polymer. The polymer has ester functional group with two different
> atom
> > > > types O and OS according to GAFF. It has also a side chain with
> > ethereal
> > > > oxygen which has the same atom type as the ester part. How can I
> > specify
> > > > the O of the side chain in the index file to tell it apart from the
> > > other O
> > > > atoms?
> > > > Besides there are around 500 of this atom in the system so changing
> > > > something manually is not a good option either.
> > > >
> > > > Best regards,
> > > > Mahsa
> > > > --
> > > > 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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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Dear Mark,

Could you please comment on my previous question? I would really appreciate
it.

Best regards,
Mahsa

On Sat, Aug 11, 2018 at 12:52 PM, Mahsa  wrote:

> Hi Mark,
>
> Thank you for your reply!
>
> I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> based on the atom types which worked very well. The only problem is I need
> to also compute the RDF for the O of the side chain with the same atom type
> as the ester O in the polymer. Then with this approach I get both O types
> in a group while I should have them separately. Could you help me with this
> problem? I don't know how to specify this one for the RDF calculations.
>
> Best regards,
> Mahsa
>
>
>
>
>
> On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Making a selection with a tool like gmx select or gmx make_ndx is a good
>> way to select e.g. by atomtype.
>>
>> Mark
>>
>> On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
>>
>> > Hello,
>> >
>> > I would like to calculate the RDF between some ions and oxygen atoms of
>> a
>> > polymer. The polymer has ester functional group with two different atom
>> > types O and OS according to GAFF. It has also a side chain with ethereal
>> > oxygen which has the same atom type as the ester part. How can I specify
>> > the O of the side chain in the index file to tell it apart from the
>> other O
>> > atoms?
>> > Besides there are around 500 of this atom in the system so changing
>> > something manually is not a good option either.
>> >
>> > Best regards,
>> > Mahsa
>> > --
>> > 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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>> > 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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>>
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>
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Hi Mark,

Thank you for your reply!

I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
based on the atom types which worked very well. The only problem is I need
to also compute the RDF for the O of the side chain with the same atom type
as the ester O in the polymer. Then with this approach I get both O types
in a group while I should have them separately. Could you help me with this
problem? I don't know how to specify this one for the RDF calculations.

Best regards,
Mahsa





On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham 
wrote:

> Hi,
>
> Making a selection with a tool like gmx select or gmx make_ndx is a good
> way to select e.g. by atomtype.
>
> Mark
>
> On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
>
> > Hello,
> >
> > I would like to calculate the RDF between some ions and oxygen atoms of a
> > polymer. The polymer has ester functional group with two different atom
> > types O and OS according to GAFF. It has also a side chain with ethereal
> > oxygen which has the same atom type as the ester part. How can I specify
> > the O of the side chain in the index file to tell it apart from the
> other O
> > atoms?
> > Besides there are around 500 of this atom in the system so changing
> > something manually is not a good option either.
> >
> > Best regards,
> > Mahsa
> > --
> > 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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> > 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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>
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[gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Hello,

I would like to calculate the RDF between some ions and oxygen atoms of a
polymer. The polymer has ester functional group with two different atom
types O and OS according to GAFF. It has also a side chain with ethereal
oxygen which has the same atom type as the ester part. How can I specify
the O of the side chain in the index file to tell it apart from the other O
atoms?
Besides there are around 500 of this atom in the system so changing
something manually is not a good option either.

Best regards,
Mahsa
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Re: [gmx-users] Positive potential energy

[Mahsa]

Hi,

Thanks for your help, Justin!

Regards,
Mahsa

On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 2/25/18 10:15 AM, Mahsa wrote:
>
>> Dear Justin,
>>
>> Thank you for your reply!
>>
>> In general, is it a good approach to first use steep algorithm for EM and
>> then to further minimize do EM with cg algorithm, on the output structure?
>>
>
> I usually don't find multiple steps of EM needed in most cases, but
> occasionally. The purpose of EM is to find a plausible starting point for
> the simulation - you can never know if you're in the global minimum so it's
> a bit of working in the dark, anyway. But the gradient (max force) reports
> on that.
>
> Could you please comment on my question about the mdp files and pbc as
>> well? Actually, you mentioned here:
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2017-February/111219.html
>>
>> that for one chain of polymer in vacuum, pbc should not be considered. So,
>> for my simulation, in the first step I have one chain in vaccum and
>> eventually I want to pack the whole box with polymer chains and ions,
>> should I use pbc or not and which of the mdp files in my first post is
>> correct?
>>
>
> If you're working in the condensed phase, you need finite cutoffs, PME,
> and PBC.
>
> -Justin
>
>
> Regards,
>> Mahsa
>>
>> On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 2/25/18 9:26 AM, Mahsa wrote:
>>>
>>> Dear Mark,
>>>>
>>>> Thank you for your reply. However, this is not clear for me yet since I
>>>> read this in the tutorial from Justin:
>>>>
>>>> "There are two very important factors to evaluate and determine if EM
>>>> was
>>>> successful. The first is the potential energy (printed at the end of the
>>>> EM
>>>> process, even without -v). Epot should be negative. The second important
>>>> feature is the maximum force, Fmax, the target for which was set in
>>>> minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater
>>>> than
>>>> 1000 kJ mol-1 nm-1."
>>>>
>>>> So I don't know whether it is correct to continue a simulation which
>>>> gives
>>>> positive potential energy after the energy minimisation or not?
>>>>
>>>> And also as I mentioned in my first post (the two different mdp files),
>>>> I
>>>> don't know if I should consider pbc or not, in my simulation.
>>>>
>>>> Unfortunately, I didn't understand your answer to my previous questions.
>>>> Do
>>>> you mean that the steep integrator is not good to do energy minimization
>>>> for this type of simulation?
>>>>
>>>> Would you please help me to fix these problems?
>>>>
>>>> There is no problem. You're just comparing apples and oranges.
>>>
>>> The tutorial system is a simple protein solvated by lots of water. The
>>> potential energy function is the sum of bonded and nonbonded terms. In an
>>> aqueous protein system, the nonbonded terms (particularly water-water
>>> electrostatics) dominate the potential energy via favorable hydrogen bond
>>> interactions. The internal (bonded) parameters for all the other species
>>> are small in magnitude, by comparison, so the nonbonded terms dominate
>>> and
>>> you get a negative potential energy.
>>>
>>> In your case, you have comparatively weak nonbonded terms and larger
>>> bonded terms, such that the potential energy function is dominated by
>>> internal energy, which is by definition, positive.
>>>
>>> This is not an indication that anything is wrong with the algorithms
>>> used.
>>>
>>> -Justin
>>>
>>>
>>> Regards,
>>>
>>>> Mahsa
>>>>
>>>> On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abra...@gmail.com
>>>> >
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>>> Even if there are minima on the surface that have negative energy
>>>>> (which
>>>>> will depend how the model was developed, which you should look into)
>>>>> there's no reason to expect an arbitrary starting configuration will
>>>>> find
>>>>> one after a steepest descent search. A tangled pile of strings wi

Re: [gmx-users] Positive potential energy

[Mahsa]

Dear Justin,

Thank you for your reply!

In general, is it a good approach to first use steep algorithm for EM and
then to further minimize do EM with cg algorithm, on the output structure?

Could you please comment on my question about the mdp files and pbc as
well? Actually, you mentioned here:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html

that for one chain of polymer in vacuum, pbc should not be considered. So,
for my simulation, in the first step I have one chain in vaccum and
eventually I want to pack the whole box with polymer chains and ions,
should I use pbc or not and which of the mdp files in my first post is
correct?

Regards,
Mahsa

On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 2/25/18 9:26 AM, Mahsa wrote:
>
>> Dear Mark,
>>
>> Thank you for your reply. However, this is not clear for me yet since I
>> read this in the tutorial from Justin:
>>
>> "There are two very important factors to evaluate and determine if EM was
>> successful. The first is the potential energy (printed at the end of the
>> EM
>> process, even without -v). Epot should be negative. The second important
>> feature is the maximum force, Fmax, the target for which was set in
>> minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
>> 1000 kJ mol-1 nm-1."
>>
>> So I don't know whether it is correct to continue a simulation which gives
>> positive potential energy after the energy minimisation or not?
>>
>> And also as I mentioned in my first post (the two different mdp files), I
>> don't know if I should consider pbc or not, in my simulation.
>>
>> Unfortunately, I didn't understand your answer to my previous questions.
>> Do
>> you mean that the steep integrator is not good to do energy minimization
>> for this type of simulation?
>>
>> Would you please help me to fix these problems?
>>
>
> There is no problem. You're just comparing apples and oranges.
>
> The tutorial system is a simple protein solvated by lots of water. The
> potential energy function is the sum of bonded and nonbonded terms. In an
> aqueous protein system, the nonbonded terms (particularly water-water
> electrostatics) dominate the potential energy via favorable hydrogen bond
> interactions. The internal (bonded) parameters for all the other species
> are small in magnitude, by comparison, so the nonbonded terms dominate and
> you get a negative potential energy.
>
> In your case, you have comparatively weak nonbonded terms and larger
> bonded terms, such that the potential energy function is dominated by
> internal energy, which is by definition, positive.
>
> This is not an indication that anything is wrong with the algorithms used.
>
> -Justin
>
>
> Regards,
>> Mahsa
>>
>> On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> Even if there are minima on the surface that have negative energy (which
>>> will depend how the model was developed, which you should look into)
>>> there's no reason to expect an arbitrary starting configuration will find
>>> one after a steepest descent search. A tangled pile of strings will stay
>>> tangled.
>>>
>>> Mark
>>>
>>> On Fri, Feb 23, 2018, 23:28 Mahsa E <ebadi.ma...@gmail.com> wrote:
>>>
>>> Hello,
>>>>
>>>> I want to simulate a box of polymer (32 chains) with salt. I started
>>>> with
>>>> one chain of the polymer in the box. However, after the energy
>>>> minimisation, the energy is still positive. I found the discussion in
>>>> the
>>>> link below very similar to the problem I have:
>>>>
>>>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>>>> /2017-February/111219.html
>>>>
>>>> and tried the tips from Justin in the link but I still get positive
>>>>
>>> energy.
>>>
>>>> This is my first MDP file:
>>>>
>>>> define   =
>>>> integrator   = steep
>>>> nsteps   = -1
>>>> nstcgsteep   = 10
>>>> constraints  = none
>>>> lincs_order  = 8
>>>> emtol= 20
>>>> emstep   = 0.01
>>>> comm-mode= Linear
>>>> nstcomm  = 1
>>>> nstcalcenergy= 1
>>>> ;

Re: [gmx-users] Positive potential energy

[Mahsa]

Dear Mark,

Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:

"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the end of the EM
process, even without -v). Epot should be negative. The second important
feature is the maximum force, Fmax, the target for which was set in
minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
1000 kJ mol-1 nm-1."

So I don't know whether it is correct to continue a simulation which gives
positive potential energy after the energy minimisation or not?

And also as I mentioned in my first post (the two different mdp files), I
don't know if I should consider pbc or not, in my simulation.

Unfortunately, I didn't understand your answer to my previous questions. Do
you mean that the steep integrator is not good to do energy minimization
for this type of simulation?

Would you please help me to fix these problems?

Regards,
Mahsa

On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Even if there are minima on the surface that have negative energy (which
> will depend how the model was developed, which you should look into)
> there's no reason to expect an arbitrary starting configuration will find
> one after a steepest descent search. A tangled pile of strings will stay
> tangled.
>
> Mark
>
> On Fri, Feb 23, 2018, 23:28 Mahsa E <ebadi.ma...@gmail.com> wrote:
>
> > Hello,
> >
> > I want to simulate a box of polymer (32 chains) with salt. I started with
> > one chain of the polymer in the box. However, after the energy
> > minimisation, the energy is still positive. I found the discussion in the
> > link below very similar to the problem I have:
> >
> > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
> > /2017-February/111219.html
> >
> > and tried the tips from Justin in the link but I still get positive
> energy.
> >
> > This is my first MDP file:
> >
> > define   =
> > integrator   = steep
> > nsteps   = -1
> > nstcgsteep   = 10
> > constraints  = none
> > lincs_order  = 8
> > emtol= 20
> > emstep   = 0.01
> > comm-mode= Linear
> > nstcomm  = 1
> > nstcalcenergy= 1
> > ; Output frequency for energies to log file and energy file
> > nstlog   = 1
> > nstenergy= 1
> > ns_type  = grid
> > cutoff-scheme= verlet
> > coulombtype  = PME
> > nstlist  = 10
> > rlist= 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
> > Tcoupl   = no
> > Pcoupl   = no
> > gen_vel  = no
> > nstxout  = 1
> > pbc  = xyz
> >
> > and this is the second one which I tried to follow the tips from the link
> > mentioned  above:
> >
> > define   =
> > integrator   = steep
> > nsteps   = -1
> > nstcgsteep   = 10
> > constraints  = none
> > lincs_order  = 8
> > emtol= 20
> > emstep   = 0.01
> > comm-mode= Linear
> > nstcomm  = 1
> > nstcalcenergy= 1
> > ; Output frequency for energies to log file and energy file
> > nstlog   = 1
> > nstenergy= 1
> > ns_type  = grid
> > cutoff-scheme= group
> > coulombtype  = cut-off
> > nstlist  = 0
> > rlist= 0
> > rcoulomb = 0
> > rvdw = 0
> > Tcoupl   = no
> > Pcoupl   = no
> > gen_vel  = no
> > nstxout  = 1
> > pbc  = no
> >
> > My questions are:
> >
> > - I'm not sure if either of these MDP files are correct for the system
> I'm
> > trying to simulate?
> >
> > - Why energy is positive in this simulation? Is there something
> > fundamentally wrong in the simulation which I'm not aware of?
> >
> > Regards,
> > Mahsa
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mai

[gmx-users] Positive potential energy

[Mahsa E]

Hello,

I want to simulate a box of polymer (32 chains) with salt. I started with
one chain of the polymer in the box. However, after the energy
minimisation, the energy is still positive. I found the discussion in the
link below very similar to the problem I have:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html

and tried the tips from Justin in the link but I still get positive energy.

This is my first MDP file:

define   =
integrator   = steep
nsteps   = -1
nstcgsteep   = 10
constraints  = none
lincs_order  = 8
emtol= 20
emstep   = 0.01
comm-mode= Linear
nstcomm  = 1
nstcalcenergy= 1
; Output frequency for energies to log file and energy file
nstlog   = 1
nstenergy= 1
ns_type  = grid
cutoff-scheme= verlet
coulombtype  = PME
nstlist  = 10
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.0
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 1
pbc  = xyz

and this is the second one which I tried to follow the tips from the link
mentioned  above:

define   =
integrator   = steep
nsteps   = -1
nstcgsteep   = 10
constraints  = none
lincs_order  = 8
emtol= 20
emstep   = 0.01
comm-mode= Linear
nstcomm  = 1
nstcalcenergy= 1
; Output frequency for energies to log file and energy file
nstlog   = 1
nstenergy= 1
ns_type  = grid
cutoff-scheme= group
coulombtype  = cut-off
nstlist  = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 1
pbc  = no

My questions are:

- I'm not sure if either of these MDP files are correct for the system I'm
trying to simulate?

- Why energy is positive in this simulation? Is there something
fundamentally wrong in the simulation which I'm not aware of?

Regards,
Mahsa
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Re: [gmx-users] Calculate RDF within a certain distance from atom

[Mahsa E]

Hi,

I think the selection keywords in the manual are helpful:

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html#selection-examples

/Mahsa


On Tue, Feb 20, 2018 at 5:53 PM, Dilip H N <cy16f01.di...@nitk.edu.in>
wrote:

> Hello,
> How to get RDF within a certain distance..??
>
> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
> atoms within 0.7nm of C-alpha (Calpha-Ow).
>
> how can i get it from in-house gmx rdf command...??
>
> Any suggestions are appreciated...
>
> Thank you.
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D. Student
>
>
>
> ‌
> <https://mailtrack.io/> Sent with Mailtrack
> <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
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Re: [gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Thank you very much for the links!

Best regards,
Mahsa

On Mon, Sep 18, 2017 at 1:30 AM, Dallas Warren <dallas.war...@monash.edu>
wrote:

> These two images will help you see what is going on:
>
> https://twitter.com/dr_dbw/status/909559339366572032 - shows a
> molecule that appears to be outside the box.
>
> https://twitter.com/dr_dbw/status/909559783291723776 - however, that
> molecule actually enters through the opposite face of the box.
> 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 18 September 2017 at 09:22, Mahsa E <ebadi.ma...@gmail.com> wrote:
> > Thank you for you quick reply, Justin and Dallas! Very good point!
> >
> > Best regards,
> > Mahsa
> >
> >
> >
> >
> >
> > On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> >>
> >>
> >> On 9/17/17 6:57 PM, Mahsa E wrote:
> >>
> >>> Could you please see the link below for the input and output simulation
> >>> box:
> >>>
> >>> https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_
> FUfvSPZxdO5WN3JnEa?dl=0
> >>>
> >>>
> >>> Actually, I thought since some of the chains went out of the simulation
> >>> box, then density have been changed. In my previous experience with
> >>> another
> >>> polymer, I didn't see this difference in the systems after the
> production
> >>> run, so I'm wondering if this is related to the stability of the
> system?
> >>>
> >>>
> >> As Dallas said, this is just a periodicity/visualization effect -
> there's
> >> no such thing as "outside" a periodic cell.
> >>
> >> Your "before MD" has "broken" molecules, i.e. all the atoms are
> visualized
> >> as being in the central image.  Your "after MD" is just those molecules
> >> made whole.  If you make the initial frame whole (trjconv -pbc whole),
> you
> >> will see a similar configuration.
> >>
> >> -Justin
> >>
> >>
> >> Best regards,
> >>> Mahsa
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren <
> dallas.war...@monash.edu
> >>> >
> >>> wrote:
> >>>
> >>> Because that is how the system changed within the simulation time?
> >>>>
> >>>> What exactly is the problem as you see it, and why do you think it is
> a
> >>>> problem?
> >>>>
> >>>> And remember, you have a periodic boundary condition that means the
> >>>> one edge of the box wraps around to the opposite one.  So "out of the
> >>>> box" is a visualisation artefact, not a "problem".
> >>>> http://www.gromacs.org/Documentation/Terminology/
> >>>> Periodic_Boundary_Conditions
> >>>> 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 18 September 2017 at 06:31, Mahsa E <ebadi.ma...@gmail.com> wrote:
> >>>>
> >>>>> Dear gmx-users,
> >>>>>
> >>>>> I did a 200 ns production md run in NVT ensemble for a simulation
> box of
> >>>>> polymer chains. Before this step, I did the energy minimisation, NVT
> and
> >>>>> NPT equilibration on the system. The problem is after the production
> >>>>>
> >>>> run, I
> >>>>
> >>>>> don't get the initial equilibrated packed box of polymer and it seems
> >>>>>
> >>>> more
> >>>>
> >>>>> like a circular shape with some parts of the chains out of the box.
> What
> >&

Re: [gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Thank you for you quick reply, Justin and Dallas! Very good point!

Best regards,
Mahsa





On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/17/17 6:57 PM, Mahsa E wrote:
>
>> Could you please see the link below for the input and output simulation
>> box:
>>
>> https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0
>>
>>
>> Actually, I thought since some of the chains went out of the simulation
>> box, then density have been changed. In my previous experience with
>> another
>> polymer, I didn't see this difference in the systems after the production
>> run, so I'm wondering if this is related to the stability of the system?
>>
>>
> As Dallas said, this is just a periodicity/visualization effect - there's
> no such thing as "outside" a periodic cell.
>
> Your "before MD" has "broken" molecules, i.e. all the atoms are visualized
> as being in the central image.  Your "after MD" is just those molecules
> made whole.  If you make the initial frame whole (trjconv -pbc whole), you
> will see a similar configuration.
>
> -Justin
>
>
> Best regards,
>> Mahsa
>>
>>
>>
>>
>>
>> On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren <dallas.war...@monash.edu
>> >
>> wrote:
>>
>> Because that is how the system changed within the simulation time?
>>>
>>> What exactly is the problem as you see it, and why do you think it is a
>>> problem?
>>>
>>> And remember, you have a periodic boundary condition that means the
>>> one edge of the box wraps around to the opposite one.  So "out of the
>>> box" is a visualisation artefact, not a "problem".
>>> http://www.gromacs.org/Documentation/Terminology/
>>> Periodic_Boundary_Conditions
>>> 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 18 September 2017 at 06:31, Mahsa E <ebadi.ma...@gmail.com> wrote:
>>>
>>>> Dear gmx-users,
>>>>
>>>> I did a 200 ns production md run in NVT ensemble for a simulation box of
>>>> polymer chains. Before this step, I did the energy minimisation, NVT and
>>>> NPT equilibration on the system. The problem is after the production
>>>>
>>> run, I
>>>
>>>> don't get the initial equilibrated packed box of polymer and it seems
>>>>
>>> more
>>>
>>>> like a circular shape with some parts of the chains out of the box. What
>>>>
>>> is
>>>
>>>> the reason for getting this result?
>>>> For the MD run I used the mdp file below:
>>>>
>>>> ; 7.3.2 Preprocessing
>>>>
>>>> ;define  =   ; defines to pass to the preprocessor
>>>>
>>>>
>>>> ; 7.3.3 Run Control
>>>>
>>>> integrator  = md; md integrator
>>>>
>>>> tinit   = 0 ; [ps] starting time for
>>>>
>>> run
>>>
>>>>
>>>> dt  = 0.002 ; [ps] time step for
>>>> integration
>>>>
>>>> nsteps  = 1; maximum number of
>>>> steps to integrate, 0.002 * 1 = 20 ps
>>>>
>>>> comm_mode   = Linear; remove center of mass
>>>> translation
>>>>
>>>> nstcomm = 100 ; [steps] frequency of
>>>> mass motion removal
>>>>
>>>> ;comm_grps   = Protein Non-Protein   ; group(s) for center
>>>> of
>>>> mass motion removal
>>>>
>>>>
>>>> ; 7.3.8 Output Control
>>>>
>>>> nstxout = 0 ; [steps] freq to write coordinates
>>>>
>>> to
>>>
>>>> trajectory
>>>>
>>>> nstvout = 0 ; [steps] freq to write velocities
>>>> to
>>>> tr

Re: [gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Could you please see the link below for the input and output simulation box:

https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_FUfvSPZxdO5WN3JnEa?dl=0


Actually, I thought since some of the chains went out of the simulation
box, then density have been changed. In my previous experience with another
polymer, I didn't see this difference in the systems after the production
run, so I'm wondering if this is related to the stability of the system?

Best regards,
Mahsa





On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren <dallas.war...@monash.edu>
wrote:

> Because that is how the system changed within the simulation time?
>
> What exactly is the problem as you see it, and why do you think it is a
> problem?
>
> And remember, you have a periodic boundary condition that means the
> one edge of the box wraps around to the opposite one.  So "out of the
> box" is a visualisation artefact, not a "problem".
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
> 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 18 September 2017 at 06:31, Mahsa E <ebadi.ma...@gmail.com> wrote:
> > Dear gmx-users,
> >
> > I did a 200 ns production md run in NVT ensemble for a simulation box of
> > polymer chains. Before this step, I did the energy minimisation, NVT and
> > NPT equilibration on the system. The problem is after the production
> run, I
> > don't get the initial equilibrated packed box of polymer and it seems
> more
> > like a circular shape with some parts of the chains out of the box. What
> is
> > the reason for getting this result?
> > For the MD run I used the mdp file below:
> >
> > ; 7.3.2 Preprocessing
> >
> > ;define  =   ; defines to pass to the preprocessor
> >
> >
> > ; 7.3.3 Run Control
> >
> > integrator  = md; md integrator
> >
> > tinit   = 0 ; [ps] starting time for
> run
> >
> > dt  = 0.002 ; [ps] time step for
> > integration
> >
> > nsteps  = 1; maximum number of
> > steps to integrate, 0.002 * 1 = 20 ps
> >
> > comm_mode   = Linear; remove center of mass
> > translation
> >
> > nstcomm = 100 ; [steps] frequency of
> > mass motion removal
> >
> > ;comm_grps   = Protein Non-Protein   ; group(s) for center of
> > mass motion removal
> >
> >
> > ; 7.3.8 Output Control
> >
> > nstxout = 0 ; [steps] freq to write coordinates
> to
> > trajectory
> >
> > nstvout = 0 ; [steps] freq to write velocities to
> > trajectory
> >
> > nstfout = 0 ; [steps] freq to write forces to
> > trajectory
> >
> > nstlog  = 1000   ; [steps] freq to write energies
> > to log file
> >
> > nstenergy   = 1000   ; [steps] freq to write energies
> > to energy file
> >
> > nstxtcout   = 1000   ; [steps] freq to write
> > coordinates to xtc trajectory
> >
> > xtc_precision   = 1000  ; [real] precision to write xtc
> > trajectory
> >
> > xtc_grps= System; group(s) to write to xtc
> > trajectory
> >
> > energygrps  = System; group(s) to write to energy
> file
> >
> > cutoff-scheme= verlet
> >
> > ; 7.3.9 Neighbor Searching
> >
> > nstlist = 20 ; [steps] freq to update
> neighbor
> > list
> >
> > ns_type = grid  ; method of updating neighbor
> list
> >
> > pbc = xyz   ; periodic boundary conditions in
> > all directions
> >
> > rlist   = 0.8   ; [nm] cut-off distance for the
> > short-range neighbor list
> >
> >
> > ; 7.3.10 Electrostatics
> >
> > coulombtype = PME   ; Particle-Mesh Ewald
> electrostatics
> >
> > rcoulomb= 1.2   ; [nm] distance for Coulomb
> cut-off
> >
> >
> &

[gmx-users] Changes in the simulation box after the production run

[Mahsa E]

Dear gmx-users,

I did a 200 ns production md run in NVT ensemble for a simulation box of
polymer chains. Before this step, I did the energy minimisation, NVT and
NPT equilibration on the system. The problem is after the production run, I
don't get the initial equilibrated packed box of polymer and it seems more
like a circular shape with some parts of the chains out of the box. What is
the reason for getting this result?
For the MD run I used the mdp file below:

; 7.3.2 Preprocessing

;define  =   ; defines to pass to the preprocessor


; 7.3.3 Run Control

integrator  = md; md integrator

tinit   = 0 ; [ps] starting time for run

dt  = 0.002 ; [ps] time step for
integration

nsteps  = 1; maximum number of
steps to integrate, 0.002 * 1 = 20 ps

comm_mode   = Linear; remove center of mass
translation

nstcomm = 100 ; [steps] frequency of
mass motion removal

;comm_grps   = Protein Non-Protein   ; group(s) for center of
mass motion removal


; 7.3.8 Output Control

nstxout = 0 ; [steps] freq to write coordinates to
trajectory

nstvout = 0 ; [steps] freq to write velocities to
trajectory

nstfout = 0 ; [steps] freq to write forces to
trajectory

nstlog  = 1000   ; [steps] freq to write energies
to log file

nstenergy   = 1000   ; [steps] freq to write energies
to energy file

nstxtcout   = 1000   ; [steps] freq to write
coordinates to xtc trajectory

xtc_precision   = 1000  ; [real] precision to write xtc
trajectory

xtc_grps= System; group(s) to write to xtc
trajectory

energygrps  = System; group(s) to write to energy file

cutoff-scheme= verlet

; 7.3.9 Neighbor Searching

nstlist = 20 ; [steps] freq to update neighbor
list

ns_type = grid  ; method of updating neighbor list

pbc = xyz   ; periodic boundary conditions in
all directions

rlist   = 0.8   ; [nm] cut-off distance for the
short-range neighbor list


; 7.3.10 Electrostatics

coulombtype = PME   ; Particle-Mesh Ewald electrostatics

rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off


; 7.3.11 VdW

vdwtype = cut-off   ; twin-range cut-off with rlist
where rvdw >= rlist

vdw-modifier = potential-switch

rvdw-switch  = 1.1

rvdw= 1.2   ; [nm] distance for LJ cut-off

DispCorr= EnerPres  ; apply long range dispersion
corrections


; 7.3.13 Ewald

fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME

pme_order   = 4 ; interpolation order for PME, 4 =
cubic

ewald_rtol  = 1e-6  ; relative strength of
Ewald-shifted potential at rcoulomb

ewald-rtol-lj= 0.001

lj-pme-comb-rule = Geometric

ewald-geometry   = 3d

epsilon_surface  = 0


; 7.3.14 Temperature Coupling

tcoupl  = v-rescale; temperature
coupling with

tc_grps = system; groups to couple seperately to
temperature bath

tau_t   = 0.1; [ps] time constant
for coupling

ref_t   = 303; [K] reference
temperature for coupling


; 7.3.17 Velocity Generation

gen_vel = no   ; generate velocities according to
Maxwell distribution of temperature

gen_temp= 303   ; [K] temperature for Maxwell
distribution

gen_seed= -1; [integer] used to initialize
random generator for random velocities


; 7.3.18 Bonds

constraints = h-bonds

constraint_algorithm= LINCS ; LINear Constraint Solver

continuation= no; no = apply constraints to the
start configuration

lincs_order = 4 ; highest order in the expansion of
the contraint coupling matrix

lincs_iter  = 1 ; number of iterations to correct
for rotational lengthening

lincs_warnangle = 30; [degrees] maximum angle that a
bond can rotate before LINCS will complain

Best regards,

Mahsa
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Re: [gmx-users] Generating topology file for a long polymer chain

[Mahsa E]

Thank you for your help!

Best regards,
Mahsa

On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/6/17 8:35 PM, Mahsa E wrote:
>
>> Hello Justin,
>>
>> Thank you so much for your reply!
>>
>> I followed what you suggested. Please correct me if I misunderstood;
>>
>> 1- I used acpype to generate the parameters (charges, atom types, and
>> bonded parameters) for the monomer, which create many files including
>> GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files.
>>
>> 2- Then I build the dimer and used the conformer search in Marvin/Avogadro
>> to find the best conformer for the dimer (.xyz or .pdb).
>>
>>
> You'll need to parametrize (at minimum) dihedral terms around the bond
> connecting the monomers in the dimer.  Finding a single conformer doesn't
> give you that information.  You need to back up and consult the primary
> literature for how your force field should work and how things should be
> parametrized (right level of theory, expected level of agreement, etc).
> This is not something that either acepype or GROMACS are going to give you;
> it usually requires QM work and parameter fitting.
>
> 3- The missing part for me is from this step. What should I do after
>> running acpype for the dimer ?
>> how to use the information from previous steps to generate the .itp file
>> for a longer chain of polymer (like 25 units)?
>>
>>
> If you've parametrized all possible internal parameters in small model
> systems, there's nothing special about larger ones; they're just small
> model compounds linked together, so you've already done everything.  Just
> use pdb2gmx with suitable .rtp files:
>
> http://www.gromacs.org/Documentation/How-tos/Polymers
>
> -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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>
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Re: [gmx-users] Generating topology file for a long polymer chain

[Mahsa E]

Hello Justin,

Thank you so much for your reply!

I followed what you suggested. Please correct me if I misunderstood;

1- I used acpype to generate the parameters (charges, atom types, and
bonded parameters) for the monomer, which create many files including
GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files.

2- Then I build the dimer and used the conformer search in Marvin/Avogadro
to find the best conformer for the dimer (.xyz or .pdb).

3- The missing part for me is from this step. What should I do after
running acpype for the dimer ?
how to use the information from previous steps to generate the .itp file
for a longer chain of polymer (like 25 units)?

 Your kind help on this is very much appreciated.

Best regards,
Mahsa

On Sun, Aug 6, 2017 at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/5/17 8:12 AM, Mahsa E wrote:
>
>> Dear gmx-users,
>>
>> I am trying to build a polymer box from scratch and generate the required
>> input files. So far, I did these steps:
>> 1. built a chain of the polymer
>> 2. run ACPYPE to generate the topology file...
>> However, since the chain is long, it took so long time with ACPYPE and the
>> calculation is timed out without convergence.
>>
>> - Is it possible to restart the ACPYPE calculation?
>>
>> I read in some tutorials that it is also possible to run the ACPYPE
>> calculations for the monomeric unit instead and repeat its parameters for
>> the whole chain. How is it possible? The polymer chain may have a
>> conformation with different angles and dihedrals than in the monomer.
>> In general, how can I use the topology file of a monomer for the longer
>> chain of a polymer ?
>> Could you please advise me?
>>
>>
> You parametrize the monomer (charges, atom types, bonded parameters), then
> build up by doing, e.g. conformational energy scans of dihedral rotations
> between the dimer.  That way you can build a proper model of the whole
> polymer.  Do not try to parametrize an entire polymer at once; you'll end
> up with a conformation-specific solution for a given geometry, if you can
> even get it to work at all.
>
> -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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[gmx-users] Generating topology file for a long polymer chain

[Mahsa E]

Dear gmx-users,

I am trying to build a polymer box from scratch and generate the required
input files. So far, I did these steps:
1. built a chain of the polymer
2. run ACPYPE to generate the topology file...
However, since the chain is long, it took so long time with ACPYPE and the
calculation is timed out without convergence.

- Is it possible to restart the ACPYPE calculation?

I read in some tutorials that it is also possible to run the ACPYPE
calculations for the monomeric unit instead and repeat its parameters for
the whole chain. How is it possible? The polymer chain may have a
conformation with different angles and dihedrals than in the monomer.
In general, how can I use the topology file of a monomer for the longer
chain of a polymer?
Could you please advise me?

Best regards,
Mahsa
-- 
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[gmx-users] Generating topology file for a long polymer chain

[Mahsa E]

Dear gmx-users,

I am trying to build a polymer box from scratch and generate the required
input files. So far, I did these steps:
1. built a chain of the polymer
2. run ACPYPE to generate the topology file...
However, since the chain is long, it took so long time with ACPYPE and the
calculation is timed out without convergence.

- Is it possible to restart the ACPYPE calculation?

I read in some tutorials that it is also possible to run the ACPYPE
calculations for the monomeric unit instead and repeat its parameters for
the whole chain. How is it possible? The polymer chain may have a
conformation with different angles and dihedrals than in the monomer.
In general, how can I use the topology file of a monomer for the longer
chain of a polymer ?
Could you please advise me?

Best regards,
Mahsa
-- 
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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