[gmx-users] Glycosylation of ASN

[Naba]

Hi,

Have you tried reducing the timestep in mdp?

Yes, I tried. But no hope.


On Mon, May 4, 2020, 2:52 AM Naba https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:

>* Dear users and developers,
*>>* I have spent extensive amount of time to model glycosylated ASN residues
*>* covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using
*>* Amber99SB-ILDN force field. Though there may be easy way to do this
*>* with CHARMM-GUI, I want it for Amber force field for maintaining
*>* consistency of force field usage with respect to the other sets of
*>* simulations I have performed already.
*>>* I have gone through several post on this and planned to give a try. So,
*>* I've extracted a pair of covalently bound ASN and NAG from the PDB file
*>* where they present. I have generated the NAG topology parameters using
*>* GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp,
*>* ffbonded.itp and all required files as instructed in the manual section 5.6
*>* and it was successful in equilibrations. After completion of NVT and NPT
*>* successfully for 500 ps each, around 7 ns of the production MD, I am
*>* encountered with warnings and ultimately fatal error like following:
*>>* Step 3869783, time 7739.57 (ps)  LINCS WARNING
*>* relative constraint deviation after LINCS:
*>* rms 0.03, max 0.13 (between atoms 23 and 24)
*>* bonds that rotated more than 30 degrees:
*>*  atom 1 atom 2  angle  previous, current, constraint length
*>*  21 22   67.60.1090   0.1090  0.1090
*>*  21 22   67.60.1090   0.1090  0.1090
*>*  21 22   67.60.1090   0.1090  0.1090
*>*  21 22   67.60.1090   0.1090  0.1090
*>*  21 22   67.60.1090   0.1090  0.1090
*>* ...
*>* ...
*>* ...
*>>* for many steps
*>>* and then
*>>* step 3869795: One or more water molecules can not be settled.
*>* Check for bad contacts and/or reduce the timestep if appropriate.
*>* Wrote pdb files with previous and current coordinates
*>* Segmentation fault  (core dumped)
*>>* I checked it repeatedly by minimizing the structure several times using
*>* other software including a series of vacuum minimization with
*>* GROMACS-2019.5 using steepest descent and conjugate gradient minimizers.
*>* But no success.
*>>* Please try to give a way to resolve it. If possible.
*>>* Regards,
*>* Naba*


On Mon, 4 May, 2020, 02:51 Naba,  wrote:

> Dear users and developers,
>
> I have spent extensive amount of time to model glycosylated ASN residues
> covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein
> using Amber99SB-ILDN force field. Though there may be easy way to do this
> with CHARMM-GUI, I want it for Amber force field for maintaining
> consistency of force field usage with respect to the other sets of
> simulations I have performed already.
>
> I have gone through several post on this and planned to give a try. So,
> I've extracted a pair of covalently bound ASN and NAG from the PDB file
> where they present. I have generated the NAG topology parameters using
> GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp,
> ffbonded.itp and all required files as instructed in the manual section 5.6
> and it was successful in equilibrations. After completion of NVT and NPT
> successfully for 500 ps each, around 7 ns of the production MD, I am
> encountered with warnings and ultimately fatal error like following:
>
> Step 3869783, time 7739.57 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.03, max 0.13 (between atoms 23 and 24)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
> ...
> ...
> ...
>
> for many steps
>
> and then
>
> step 3869795: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Segmentation fault  (core dumped)
>
> I checked it repeatedly by minimizing the structure several times using
> other software including a series of vacuum minimization with
> GROMACS-2019.5 using steepest descent and conjugate gradient minimizers.
> But no success.
>
> Please try to give a way to resolve it. If possible.
>
> Regards,
> Naba
>
>
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infr

[gmx-users] Glycosylation of ASN

[Naba]

Dear users and developers,

I have spent extensive amount of time to model glycosylated ASN residues
covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using
Amber99SB-ILDN force field. Though there may be easy way to do this
with CHARMM-GUI, I want it for Amber force field for maintaining
consistency of force field usage with respect to the other sets of
simulations I have performed already.

I have gone through several post on this and planned to give a try. So,
I've extracted a pair of covalently bound ASN and NAG from the PDB file
where they present. I have generated the NAG topology parameters using
GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp,
ffbonded.itp and all required files as instructed in the manual section 5.6
and it was successful in equilibrations. After completion of NVT and NPT
successfully for 500 ps each, around 7 ns of the production MD, I am
encountered with warnings and ultimately fatal error like following:

Step 3869783, time 7739.57 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.03, max 0.13 (between atoms 23 and 24)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 22   67.60.1090   0.1090  0.1090
 21 22   67.60.1090   0.1090  0.1090
 21 22   67.60.1090   0.1090  0.1090
 21 22   67.60.1090   0.1090  0.1090
 21 22   67.60.1090   0.1090  0.1090
...
...
...

for many steps

and then

step 3869795: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault  (core dumped)

I checked it repeatedly by minimizing the structure several times using
other software including a series of vacuum minimization with
GROMACS-2019.5 using steepest descent and conjugate gradient minimizers.
But no success.

Please try to give a way to resolve it. If possible.

Regards,
Naba


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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[gmx-users] Water permeation through a channel of membrane protein

[Naba]

Dear gromacs users & developers,

I searched about the topic in the subject-line in the mailing list. But I
couldn't find possible solution. I came to know that gmx select can be
effectively used to calculate the number of water molecules within a porin
channel, but I am not getting the clue to do that.

For instance, if my channel is defined by the residues SER65, GLY66, HIS68,
ASN70, VAL73, THR74, MET77, GLN82, ILE83, TYR91 and so on, how to use gmx
select to calculate the upper and lower boundaries and number of water
molecules in side the channel?

Please help.
For reference, here is my gro file:
https://www.dropbox.com/l/scl/AACHT3J_YHEPyPSQRWn2YOmaUNwRY1eRPQw

Regards
Naba



Nabajyoti Goswami

Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
Gromacs Users mailing list

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[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

[Naba]

Dear Dr. Justin,

Thanks a lot for suggestions and hints.

I issued:

gmx dump -s npt.tpr

to check the velocities.

Following are last few lines after execution of the above command:

   v[120488]={-8.24012e-01, -3.10189e-01,  3.53090e-01}
   v[120489]={-5.70083e-02,  6.79958e-01,  1.43155e+00}
   v[120490]={ 4.60961e-01,  8.73407e-02, -1.26087e+00}
   v[120491]={ 3.43934e-01, -3.55264e-02,  5.41598e-02}
   v[120492]={-2.71835e-01,  2.20839e-01, -2.95827e-01}
   v[120493]={ 5.59665e-02,  6.66364e-01, -2.97680e-01}
   v[120494]={ 1.22493e-01,  5.81446e-01,  1.32195e-01}
Group statistics
T-Coupling  :   33740  86755  (total 120495 atoms)
Energy Mon. :   120495  (total 120495 atoms)
Acceleration:   120495  (total 120495 atoms)
Freeze  :   120495  (total 120495 atoms)
User1   :   120495  (total 120495 atoms)
User2   :   120495  (total 120495 atoms)
VCM :   33740  86755  (total 120495 atoms)
Compressed X:   120495  (total 120495 atoms)
Or. Res. Fit:   120495  (total 120495 atoms)
QMMM:   120495  (total 120495 atoms)
   -

Using -maxwarn 1 in grompp, I produced the tpr file for Berendsen barostate
also and got the same output. So, I can proceed with Berendsen pressure
coupling, am I right?

Thanks & regards,
Naba




On 8/20/18 6:52 AM, Naba wrote:
> > Dear Gromacs users and developers,
> >
> > I am using Gromacs 2018.2.
> > Following the membrane protein simulation tutorial, I am planning to run
> > long simulations of a tetramer that needs larger lipid bilayer than 128
> > lipids as described in the tutorial. So, I have replicated the
> > pre-equilibrated POPC bilayer of 128 lipids from lipidbook (
> > https://lipidbook.bioch.ox.ac.uk/lipid/) to get a larger bilayer of 512
> > lipids using genconf. Moreover, I have extended gromos54a7_lipid.ff
> > forcefield to Berger lipid parameters for long membrane protein
> > simulations. I have set 10 ns for NVT and 20 ns for NPT equilibration.
> > NVT simulation ran successfully, but when I reached to NPT equilibration,
> > grompp showed me a note like the following:
> > "You are combining position restraints with Parrinello-Rahman pressure
> >coupling, which can lead to instabilities. If you really want to
> combine
> >position restraints with pressure coupling, we suggest to use
> Berendsen
> >pressure coupling instead."
>
> I think this note is a bit imprecise. grompp is guessing that the
> combination of Parrinello-Rahman and restraints implies equilibration,
> and it should really say so, or otherwise do a more rigorous check to
> see if velocities are being generated. In principle, there shouldn't be
> anything wrong with this approach, but Parrinello-Rahman *usually* isn't
> the best choice for equilibration.
>

> When I used Berendsen pressure coupling, grompp terminated with a warning
> > as:
> > "Using Berendsen pressure coupling invalidates the true ensemble for the
> >thermostat"
>
> This only matters for production runs. The Berendsen method should never
> be used for actual data collection. For equilibration, it's perfectly
> fine because you're going to throw this time out, anyway.
>
> -Justin
>
> > What to do with this? Can I proceed with the note using Parrinello-Rahman
> > pressure coupling? Please help.
> >
> > Following is the mdp parameters I have used:
> >
> > title   = NPT Equilibration for KALP15-DPPC
> > define  = -DPOSRES  ; position restrain the protein
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 1000; 2 * 1000 = 2 ps (20 ns)
> > dt  = 0.002 ; 2 fs
> > cutoff-scheme = verlet
> > ; Output control
> > nstxout = 2500   ; save coordinates every 5 ps
> > nstvout = 2500   ; save velocities every 5 ps
> > nstenergy   = 2500   ; save energies every 5 ps
> > nstlog  = 2500   ; update log file every 5 ps
> > ; Bond parameters
> > continuation= yes   ; Restarting after NVT
> > constraint_algorithm= lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter  = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid  ; search neighboring grid cels
> > nstlist = 5 ; 10 fs
> > rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
> > rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
> > rvdw= 1.2   ; short-range van der Waals cutoff (in nm)

[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

[Naba]

Dear Gromacs users and developers,

I am using Gromacs 2018.2.
Following the membrane protein simulation tutorial, I am planning to run
long simulations of a tetramer that needs larger lipid bilayer than 128
lipids as described in the tutorial. So, I have replicated the
pre-equilibrated POPC bilayer of 128 lipids from lipidbook (
https://lipidbook.bioch.ox.ac.uk/lipid/) to get a larger bilayer of 512
lipids using genconf. Moreover, I have extended gromos54a7_lipid.ff
forcefield to Berger lipid parameters for long membrane protein
simulations. I have set 10 ns for NVT and 20 ns for NPT equilibration.
NVT simulation ran successfully, but when I reached to NPT equilibration,
grompp showed me a note like the following:
"You are combining position restraints with Parrinello-Rahman pressure
  coupling, which can lead to instabilities. If you really want to combine
  position restraints with pressure coupling, we suggest to use Berendsen
  pressure coupling instead."

When I used Berendsen pressure coupling, grompp terminated with a warning
as:
"Using Berendsen pressure coupling invalidates the true ensemble for the
  thermostat"

What to do with this? Can I proceed with the note using Parrinello-Rahman
pressure coupling? Please help.

Following is the mdp parameters I have used:

title   = NPT Equilibration for KALP15-DPPC
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 2 * 1000 = 2 ps (20 ns)
dt  = 0.002 ; 2 fs
cutoff-scheme = verlet
; Output control
nstxout = 2500   ; save coordinates every 5 ps
nstvout = 2500   ; save velocities every 5 ps
nstenergy   = 2500   ; save energies every 5 ps
nstlog  = 2500   ; update log file every 5 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps = Protein_POPC  Water_and_ions  ; two coupling groups -
more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 300   300 ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_POPC Water_and_ions
; Scale COM of reference coordinates
refcoord_scaling = com
nstcalcenergy = 1
nhchainlength = 1


Thank in advance.

Regards,

Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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Re: [gmx-users] Pulling two groups in opposite direction

[Naba]

>
> On 5/17/18 1:39 AM, Naba wrote:
> >> On 5/16/18 3:32 AM, Naba wrote:
> >>> Dear all,
> >>>
> >>> I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> >>> acids from its homodimer in opposite directions along z axis. The
> >>> interfaces of each protein chain is parallel to the z axis. I do not
> need
> >>> any restraints in this case. I have gone through the GROMACS manual and
> >>> some of the previous archived messages and set the following mdp
> options.
> >>>
> >>> ; Pull code
> >>> pull= yes
> >>> pull_ngroups= 2
> >>> pull_ncoords= 2
> >>> pull_group1_name= chain_A
> >>> pull_group2_name= chain_B
> >>> ;pull_group3_name = Protein
> >>> pull_coord1_type = umbrella
> >>> pull_coord2_type = umbrella
> >>> pull_coord1_init = 0.0
> >>> pull_coord2_init = 0.0
> >>> pull_coord1_start = yes   ; define initial COM distance > 0
> >>> pull_coord2_start = yes
> >>> pull_coord1_geometry= direction
> >>> pull_coord2_geometry= direction
> >>> pull_coord1_groups  = 2 1
> >>> pull_coord2_groups  = 1 2
> >>> pull_coord1_dim = N N Y
> >>> pull_coord2_dim = N N Y
> >> Note that pull_coord*_dim is not relevant when using "direction"
> geometry.
> >>
> >>> pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
> >>> pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
> >>> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> >>> pull_coord2_k   = 2000
> >>> pull_coord1_vec= 0.0 0.0 1.0
> >>> pull_coord2_vec= 0.0 0.0 -1.0
> >>> nstcalcenergy = 1
> >>> nhchainlength = 1
> >>>
> >>> But it fails to pull chain_A in positive z direction. However, chain_B
> is
> >>> seemed to pull in negative z direction. Someone please suggest the
> proper
> >>> way to pull two groups in opposite directions, or if there is anything
> >> that
> >>> I am missing.
> >> What is the point of pulling in two directions? Separation of two
> >> species requires only one reaction coordinate. For every action, there
> >> is an equal, but opposite reaction...
> >>
> >> -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
> >>
> >> ==
> >
> >
> > Thank you Dr. Justin.
> > Besides PMF calculations during umbrella sampling, I want to observe the
> > interacting residues while pulling both the chain in opposite directions.
> > In your tutorial you pulled only one chain for your specific case.
> Whereas
> > in my case, the point to be observed how smoothly or rigorously the
> chains
> > are interacting with their residues in interface due to the application
> of
> > two equal forces in opposite directions.
> >
> > Anyways, from your reply should I understand that pulling only one chain
> > without any restraints in only one direction will do my job? Please
> correct
> > me the mdp settings.
>
> Do not pull along only one dimension. A normal, soluble protein complex
> will rotate in space so you should pull in all three dimensions. There
> are several ways to accomplish this pulling, but indeed you only need
> one reaction coordinate to induce separation.
>
> -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
>
> ==
>
> Thank you again Dr. Justin.

How do I pull only chain so that both the chains should show sliding
movement  with respect to one another?

For your convenience here is the picture of the homodimer I am dealing
with: https://www.dropbox.com/s/6yh5vo3jcieh7rm/dummy.p

Re: [gmx-users] Pulling two groups in opposite direction

[Naba]

On Thu, May 17, 2018 at 11:09 AM, Naba <nabajyoti.gosw...@gmail.com> wrote:

> On 5/16/18 3:32 AM, Naba wrote:
>> > Dear all,
>> >
>> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
>> > acids from its homodimer in opposite directions along z axis. The
>> > interfaces of each protein chain is parallel to the z axis. I do not
>> need
>> > any restraints in this case. I have gone through the GROMACS manual and
>> > some of the previous archived messages and set the following mdp
>> options.
>> >
>> > ; Pull code
>> > pull= yes
>> > pull_ngroups= 2
>> > pull_ncoords= 2
>> > pull_group1_name= chain_A
>> > pull_group2_name= chain_B
>> > ;pull_group3_name = Protein
>> > pull_coord1_type = umbrella
>> > pull_coord2_type = umbrella
>> > pull_coord1_init = 0.0
>> > pull_coord2_init = 0.0
>> > pull_coord1_start = yes   ; define initial COM distance > 0
>> > pull_coord2_start = yes
>> > pull_coord1_geometry= direction
>> > pull_coord2_geometry= direction
>> > pull_coord1_groups  = 2 1
>> > pull_coord2_groups  = 1 2
>> > pull_coord1_dim = N N Y
>> > pull_coord2_dim = N N Y
>>
>> Note that pull_coord*_dim is not relevant when using "direction" geometry.
>>
>> > pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
>> > pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
>> > pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
>> > pull_coord2_k   = 2000
>> > pull_coord1_vec= 0.0 0.0 1.0
>> > pull_coord2_vec= 0.0 0.0 -1.0
>> > nstcalcenergy = 1
>> > nhchainlength = 1
>> >
>> > But it fails to pull chain_A in positive z direction. However, chain_B
>> is
>> > seemed to pull in negative z direction. Someone please suggest the
>> proper
>> > way to pull two groups in opposite directions, or if there is anything
>> that
>> > I am missing.
>>
>> What is the point of pulling in two directions? Separation of two
>> species requires only one reaction coordinate. For every action, there
>> is an equal, but opposite reaction...
>>
>> -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
>>
>> ==
>
>
> Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
Gromacs Users mailing list

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Re: [gmx-users] Pulling two groups in opposite direction

[Naba]

>
> On 5/16/18 3:32 AM, Naba wrote:
> > Dear all,
> >
> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> > acids from its homodimer in opposite directions along z axis. The
> > interfaces of each protein chain is parallel to the z axis. I do not need
> > any restraints in this case. I have gone through the GROMACS manual and
> > some of the previous archived messages and set the following mdp options.
> >
> > ; Pull code
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 2
> > pull_group1_name= chain_A
> > pull_group2_name= chain_B
> > ;pull_group3_name = Protein
> > pull_coord1_type = umbrella
> > pull_coord2_type = umbrella
> > pull_coord1_init = 0.0
> > pull_coord2_init = 0.0
> > pull_coord1_start = yes   ; define initial COM distance > 0
> > pull_coord2_start = yes
> > pull_coord1_geometry= direction
> > pull_coord2_geometry= direction
> > pull_coord1_groups  = 2 1
> > pull_coord2_groups  = 1 2
> > pull_coord1_dim = N N Y
> > pull_coord2_dim = N N Y
>
> Note that pull_coord*_dim is not relevant when using "direction" geometry.
>
> > pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
> > pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
> > pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> > pull_coord2_k   = 2000
> > pull_coord1_vec= 0.0 0.0 1.0
> > pull_coord2_vec= 0.0 0.0 -1.0
> > nstcalcenergy = 1
> > nhchainlength = 1
> >
> > But it fails to pull chain_A in positive z direction. However, chain_B is
> > seemed to pull in negative z direction. Someone please suggest the proper
> > way to pull two groups in opposite directions, or if there is anything
> that
> > I am missing.
>
> What is the point of pulling in two directions? Separation of two
> species requires only one reaction coordinate. For every action, there
> is an equal, but opposite reaction...
>
> -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
>
> ==



Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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[gmx-users] Pulling two groups in opposite direction

[Naba]

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y
pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything that
I am missing.

waiting for your great help..
Nabajyoti Goswami
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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[gmx-users] COM pulling

[Naba]

Dear users,

Please let me know whether it is feasible and relevant or not if I use COM
pulling for mechanical unfolding of proteins. More specifically, whether I
can define the two group within the same molecule !!

Sorry for the previous mail as it was wrongly sent to an unrelated thread.
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 74

[Naba]

Dear users,

Please let me know whether it is feasible and relevant or not if I use COM
pulling for mechanical unfolding of proteins. More specifically, whether I
can define the two group within the same molecule !!


On Wed, Aug 16, 2017 at 6:48 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: Fwd: (Justin Lemkul)
>2. (Don't know if mail worked last time)Drift with
>   groups+tabulated potential. (spere...@us.es)
>3. how to make molecular model with both ion channel and lipid
>   bilayer? (Li, Tong)
>4. Re: how to make molecular model with both ion channel and
>   lipid bilayer? (h.aliza...@znu.ac.ir)
>5. Doing restart (?farial tavakoli? ?)
>6. npt simulation error (Mohammad Zahidul Hossain Khan)
>7. Re: npt simulation error (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Tue, 15 Aug 2017 08:02:45 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Fwd:
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/15/17 1:52 AM, saranya wrote:
> > Hi,
> > I have done protein-drug simulations for 100ns. While calculating the
> hydrogen
> > bond between the protein-drug complex I am getting only 2 hydrogen bonds.
> > The number of H-bond formation is very low I have a question about is
> there
> > any influence of the drug in my protein?
> To answer that, you need to do simulations of the apo protein and
> compare whatever relevant structural metrics there are (not H-bonds, as
> these tell you about the ligand-protein interactions but nothing about
> the impact on the protein structure).
>
> -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
>
> ==
>
>
>
> --
>
> Message: 2
> Date: Tue, 15 Aug 2017 14:25:30 +0200
> From: spere...@us.es
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] (Don't know if mail worked last time)Drift with
> groups+tabulated potential.
> Message-ID: <4e579ca344c855caf935a5ebc...@us.es>
> Content-Type: text/plain; charset=US-ASCII
>
> Dear GROMACS Community,
>
> First of all, if someone got this email twice, I am sorry. It is my
> first post and I was not sure if it worked.
>
> I am trying to do a simulation using a tabulated potential which forces
> me to use the group cut-off. I get a drift in the conserved quantity of
> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
> group cutoff scheme still works correctly. I have tryed to change the
> parameters without success and in any case the ones I use seem
> reasonable (in my experience using other programs). The rdfs of the
> system look normal so I ruled out topology problems.
>
> It seems that the problem is in the group cut-off since
> when I change the tabulated potential for a regular vdw the problem
> persists. I have followed the instructions of:
>
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>
> to implement the tabulated potentials.
>
> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
>
> Thanks for your help,
>
> Sergio Perez-Conesa
>
> integrator = md
> dt = 0.001
> nsteps = 10
> init-step = 0
> cutoff-scheme = group
> nst-list = 1
> verlet-buffer-tolerance = 0.0005
> ns-type = grid
> rlist = 1.3
> pbc = xyz
> coulombtype = PME-switch
> rcoulomb = 1.
> rcoulomb-switch = 0.95
> pme-order = 4
> fourierspacing = 0.1
> ewald-rtol = 1.e-5
> vdwtype = user
> rvdw = 1.0
> DispCorr = No
> tcoupl = v-rescale
> tc-grps = System
> ;nsttcouple = 1
> tau-t = ref-t = 300.0
> constraints = all-angles
> constraint-algorithm = LINCS
> lincs_iter = 1
> lincs_order = 4
> energygrps = NA OW
> energygrp_table = NA OW
> comm-mode = linear
>
> --
>
> Message: 3
> Date: Tue, 15 Aug 2017 15:09:27 +
> From: "Li, Tong" 
> 

Re: [gmx-users] Dynamic Cross Correlation

[Naba]

Hi,

you can compute dynamic cross correlation using Bio3D package within R.
Follow this link: http://thegrantlab.org/bio3d/tutorials/trajectory-analysis

Regards,
Naba


On Sat, Oct 17, 2015 at 4:14 AM, ANAND AMITKUMAR Dharia <
adha...@berkeley.edu> wrote:

> Hello,
>
> Is there any method in GROMACS to compute dynamic cross correlation between
> different molecules. If not defined in GROMACS, what are methods people
> take to compute coupling from the trajectory data.
>
> Thanks,
> Anand Dharia
> --
> Gromacs Users mailing list
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Re: [gmx-users] Regarding gmx-user mailing list thread "Gibbs free energy landscape Vs. the stability of protein structure"

[Naba]

Dear David sir,

Is it feasible to evaluate Gibbs free energy landscape of only the
concerned loops from cartesian coordinates?
I mean to say is it feasible to extract covariance matrix of my concerned
loops from the entire trajectory and then evaluating Gibbs free energy
landscape?
OR, should I extract trajectories of each and every loops separately and
calculating extract covariance matrix of each loop and then should I see
the Gibbs free energy landscape?

On Thu, Sep 24, 2015 at 7:42 PM, David van der Spoel 
wrote:

> On 24/09/15 13:54, Nabajyoti Goswami wrote:
>
>> Sir,
>> I am a very big fan of yours and I deeply apologize for mailing this way.
>> Actually I need some outcome within a very short period of time. So, I
>> could not wait for the mailing lists answers.
>>
>> Coming to the point.. Can you please explain the tricks of dihedral PCA?
>> You answered as my sampling was far from being complete because of the
>> huge differences between my chosen temperatures 300K and 310K, then how
>> can I make some comments at least, if my results are inconclusive. So
>> far as stability point of view, how do I set my MDs?
>>
> As I said you may be sampling different part of phase space, but it could
> also be that it is something very similar in cartesian space.
> The simple recommendation is do not use dihedral PCA at all but something
> in cartesian space.
>
>>
>> I have attached another figure (3D version of the previously generated
>> figure). But I am a bit in confusion to analyze them.
>>
>> Please help a little sir.
>>
>> Regards,
>>
>> Yours truly
>>
>>
>> Nabajyoti Goswami
>>
>> Bioinformatics Infrastructure Facility
>> Department of Animal Biotechnology
>> College of Veterinary Science
>> Assam Agricultural University
>> Khanapara, Guwahati 781022
>> Assam, India
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>



-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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[gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Naba]

Dear Gromacs users and Developers,

I have performed dihedral PCA for 4 extracellular loops of a transmembrane
protein after successfully finishing 100 ns of simulation at 300 and 310 K.
I obtained figures for each loops for two different temperatures as in this
link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .

As we can see in that figure that, the loop L1 has got only one minimum at
both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
also calculated the amount of frames in percentages at their respective
minima. It seems that L2 and L3 have got more number of frames at their
minima when combined in comparison to L1. Now my question is:

Can we say that L2 and L3 are tend to be more stable at 300K than that of
L1 at the both temperatures?
Please help.
Thanks in advance.

Regards

Nabajyoti Goswami

College of Veterinary Science
Khanapara, Guwahati 781022
Assam, India.
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Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Naba]

Thank you Justin. I have to deduce some inference from this figure. Please
make me out about the following queries.

On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/21/15 4:00 AM, Naba wrote:
>
>> Dear Gromacs users and Developers,
>>
>> I have performed dihedral PCA for 4 extracellular loops of a transmembrane
>> protein after successfully finishing 100 ns of simulation at 300 and 310
>> K.
>> I obtained figures for each loops for two different temperatures as in
>> this
>> link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .
>>
>> As we can see in that figure that, the loop L1 has got only one minimum at
>> both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
>> also calculated the amount of frames in percentages at their respective
>> minima. It seems that L2 and L3 have got more number of frames at their
>> minima when combined in comparison to L1. Now my question is:
>>
>> Can we say that L2 and L3 are tend to be more stable at 300K than that of
>> L1 at the both temperatures?
>>
>
> I wouldn't make any argument about "stability" here.


Then what can be concluded from this figure? Please hint some possible
explanations.


> Conformational sampling, maybe, but the question is whether or not these
> PCs are the same between the different simulations. If you're not
> projecting one trajectory onto the other's eigenvectors, you're quite
> possibly comparing apples and oranges.
>

The PCs are same for both simulations. I followed dPCA procedure as you
have explained in http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
. To obtained the 2D projections as in the link of the figure I issued the
following command for each and every loops:

g_anaeig -v eigenvec_L*.trr -f dangle_L*.trr -s resized_loop*.gro
-first 1 -last 2 -2d 2dproj_1_2.xvg

I think, I am comparing the same projections for both the simulations.


>
> -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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>



-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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Re: [gmx-users] g_sham

[Naba]

It's working now. Thanks a lot.
One more query:
If I am interested in getting frames near the minimia and not actually on
it, how do I change the last if-statement?


On Mon, Aug 24, 2015 at 5:45 PM, Smith, Micholas D. smit...@ornl.gov
wrote:

 My bad, I had a typo, try this one:

 awk -v x=firstcoordmin -v y=secondcoordmin 'BEGIN{while(getline
 first_coordinate_file_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}}NR0{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==y){print
 $1}}}' second_coordinate_file_here.xvg

 ===
 Micholas Dean Smith, PhD.
 Post-doctoral Research Associate
 University of Tennessee/Oak Ridge National Laboratory
 Center for Molecular Biophysics

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba 
 nabajyoti.gosw...@gmail.com
 Sent: Saturday, August 22, 2015 4:16 AM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sham

 Dear Micholas,

 The awk command that you have suggested as:

 awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline 

 yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==$y){print
 $1}}' yourfile_second_coordinate_here.xvg

 is not working. It says ^ unexpected newline or end of string. I have
 supplied my coord1min, coord2min,  yourfile_first_coordinate_here.xvg and
 yourfile_second_coordinate_here.xvg.

 can you please re-write the command with correct syntax please?

 On Fri, Aug 14, 2015 at 10:44 AM, Naba nabajyoti.gosw...@gmail.com
 wrote:

  Thank you very much Micholas.
  I have actually done the second option. But I was uncertain whether I
 have
  done are all nonsense.
  From your replies it seems that I am quite close to fulfill my
 objectives.
  Meanwhile, I am about to perform dPCA for those loops as you have
 suggested
  in the previous mail.
  Thanks a lot.
 
  On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. smit...@ornl.gov
  wrote:
 
  Hi Naba,
 
  I believe you would want to do your second option if you want to include
  the contributions from all of the loops. If you are just interested in
 one
  loop, then you would do each seperately. Rule-of-thumb for these
  calculations are whatever group you use for the convariance matrix, is
 what
  you should use for the 2D projection.
 
  Hope that helps.
 
 
  ===
  Micholas Dean Smith, PhD.
  Post-doctoral Research Associate
  University of Tennessee/Oak Ridge National Laboratory
  Center for Molecular Biophysics
 
  
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba 
  nabajyoti.gosw...@gmail.com
  Sent: Thursday, August 13, 2015 4:17 AM
  To: Discussion list for GROMACS users
  Subject: Re: [gmx-users] g_sham
 
  Thanks for the reply Micholas.
 
  I read the special discussion on dPCA at your provided link. But that
 is a
  fact of small peptide penta-alanine.
  I actually completed a 100 ns simulation of a outermembrane protein (of
  239
  amino acid residues) with 284 DMPC molecules. The protein contains 4
  extracellular loops of variable lengths and I want to study the dynamics
  of
  these loops. What I wanted to confirm is:
 
  1. Is it all right if I extract covariance separately for each loops?
 OR,
  2. Should I calculate covariance of index groups of my concerned loops
 and
  then should I proceed to 2D projection (by g_anaeig)?
 
 
  On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. smit...@ornl.gov
  wrote:
 
   1. Is it feasible to obtain free energy landscape (FEL) from a 2D
   projection (using g_anaeig) of  index groups (say some loop's atoms)
  which
   are used for the least squares fit in g_covar and then selecting
 index
   group of elements that corresponds to the eigenvectors (say
  Prot-masses)?
   Or,
   Should I calculate covariance (g_covar) of my concerned loops
  separately
   and then should I go for g_sham?
  
   I am not sure if I understand, however, I think I may be able to help
 a
   litttle. g_sham is just a histograming program that inverts the
  resulting
   histogram into energy space, so using a 2D projection is a legitimate
  use.
   Indeed what you are trying to do is very similar to the steps used in
  dPCA
   (see:
  
 
 http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
   ).
  
   2. Is there any representative way to get the exact time point for
 the
   corresponding minima obtained from g_sham?
  
   If you have the time series for each of the coordinates used in the 2D
   projection you just need to scan through the 2D timeseries for values
  that
   match the minimia. e.g. If in the g_sham a minima is at coordinates
  (10,10)
   than you need to scan through the timeseries of your coordinates:
   time coord1 coord2
   1 00
   2 1   10
   3 40 400

Re: [gmx-users] g_sham

[Naba]

Dear Micholas,

The awk command that you have suggested as:

awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline 
yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==$y){print
$1}}' yourfile_second_coordinate_here.xvg

is not working. It says ^ unexpected newline or end of string. I have
supplied my coord1min, coord2min,  yourfile_first_coordinate_here.xvg and
yourfile_second_coordinate_here.xvg.

can you please re-write the command with correct syntax please?

On Fri, Aug 14, 2015 at 10:44 AM, Naba nabajyoti.gosw...@gmail.com wrote:

 Thank you very much Micholas.
 I have actually done the second option. But I was uncertain whether I have
 done are all nonsense.
 From your replies it seems that I am quite close to fulfill my objectives.
 Meanwhile, I am about to perform dPCA for those loops as you have suggested
 in the previous mail.
 Thanks a lot.

 On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. smit...@ornl.gov
 wrote:

 Hi Naba,

 I believe you would want to do your second option if you want to include
 the contributions from all of the loops. If you are just interested in one
 loop, then you would do each seperately. Rule-of-thumb for these
 calculations are whatever group you use for the convariance matrix, is what
 you should use for the 2D projection.

 Hope that helps.


 ===
 Micholas Dean Smith, PhD.
 Post-doctoral Research Associate
 University of Tennessee/Oak Ridge National Laboratory
 Center for Molecular Biophysics

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba 
 nabajyoti.gosw...@gmail.com
 Sent: Thursday, August 13, 2015 4:17 AM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sham

 Thanks for the reply Micholas.

 I read the special discussion on dPCA at your provided link. But that is a
 fact of small peptide penta-alanine.
 I actually completed a 100 ns simulation of a outermembrane protein (of
 239
 amino acid residues) with 284 DMPC molecules. The protein contains 4
 extracellular loops of variable lengths and I want to study the dynamics
 of
 these loops. What I wanted to confirm is:

 1. Is it all right if I extract covariance separately for each loops? OR,
 2. Should I calculate covariance of index groups of my concerned loops and
 then should I proceed to 2D projection (by g_anaeig)?


 On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. smit...@ornl.gov
 wrote:

  1. Is it feasible to obtain free energy landscape (FEL) from a 2D
  projection (using g_anaeig) of  index groups (say some loop's atoms)
 which
  are used for the least squares fit in g_covar and then selecting index
  group of elements that corresponds to the eigenvectors (say
 Prot-masses)?
  Or,
  Should I calculate covariance (g_covar) of my concerned loops
 separately
  and then should I go for g_sham?
 
  I am not sure if I understand, however, I think I may be able to help a
  litttle. g_sham is just a histograming program that inverts the
 resulting
  histogram into energy space, so using a 2D projection is a legitimate
 use.
  Indeed what you are trying to do is very similar to the steps used in
 dPCA
  (see:
 
 http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
  ).
 
  2. Is there any representative way to get the exact time point for the
  corresponding minima obtained from g_sham?
 
  If you have the time series for each of the coordinates used in the 2D
  projection you just need to scan through the 2D timeseries for values
 that
  match the minimia. e.g. If in the g_sham a minima is at coordinates
 (10,10)
  than you need to scan through the timeseries of your coordinates:
  time coord1 coord2
  1 00
  2 1   10
  3 40 400
  41025
  ...
  ...
  5000  10 10
  .
  6000   1010
  .
  988908   10  10
  
 
 
  where frames 988908, 5000, and 6000 are the ones you are looking for.
 You
  could extract these with
 
  awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline 
 
 yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==$y){print
  $1}}' yourfile_second_coordinate_here.xvg
 
  where you would provide the x and y coords of the minina where I have
  coord1min and coord2min.
 
  You may be more interested in getting frames near the minimia and not
  actually on it, in which case just change the last if-statement as
 needed.
 
  Hope that helps.
 
  -Micholas
 
  ===
  Micholas Dean Smith, PhD.
  Post-doctoral Research Associate
  University of Tennessee/Oak Ridge National Laboratory
  Center for Molecular Biophysics
 
  
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba

Re: [gmx-users] g_sham

[Naba]

Thanks for the reply Micholas.

I read the special discussion on dPCA at your provided link. But that is a
fact of small peptide penta-alanine.
I actually completed a 100 ns simulation of a outermembrane protein (of 239
amino acid residues) with 284 DMPC molecules. The protein contains 4
extracellular loops of variable lengths and I want to study the dynamics of
these loops. What I wanted to confirm is:

1. Is it all right if I extract covariance separately for each loops? OR,
2. Should I calculate covariance of index groups of my concerned loops and
then should I proceed to 2D projection (by g_anaeig)?


On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. smit...@ornl.gov wrote:

 1. Is it feasible to obtain free energy landscape (FEL) from a 2D
 projection (using g_anaeig) of  index groups (say some loop's atoms) which
 are used for the least squares fit in g_covar and then selecting index
 group of elements that corresponds to the eigenvectors (say Prot-masses)?
 Or,
 Should I calculate covariance (g_covar) of my concerned loops separately
 and then should I go for g_sham?

 I am not sure if I understand, however, I think I may be able to help a
 litttle. g_sham is just a histograming program that inverts the resulting
 histogram into energy space, so using a 2D projection is a legitimate use.
 Indeed what you are trying to do is very similar to the steps used in dPCA
 (see:
 http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
 ).

 2. Is there any representative way to get the exact time point for the
 corresponding minima obtained from g_sham?

 If you have the time series for each of the coordinates used in the 2D
 projection you just need to scan through the 2D timeseries for values that
 match the minimia. e.g. If in the g_sham a minima is at coordinates (10,10)
 than you need to scan through the timeseries of your coordinates:
 time coord1 coord2
 1 00
 2 1   10
 3 40 400
 41025
 ...
 ...
 5000  10 10
 .
 6000   1010
 .
 988908   10  10
 


 where frames 988908, 5000, and 6000 are the ones you are looking for. You
 could extract these with

 awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline 
 yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==$y){print
 $1}}' yourfile_second_coordinate_here.xvg

 where you would provide the x and y coords of the minina where I have
 coord1min and coord2min.

 You may be more interested in getting frames near the minimia and not
 actually on it, in which case just change the last if-statement as needed.

 Hope that helps.

 -Micholas

 ===
 Micholas Dean Smith, PhD.
 Post-doctoral Research Associate
 University of Tennessee/Oak Ridge National Laboratory
 Center for Molecular Biophysics

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba 
 nabajyoti.gosw...@gmail.com
 Sent: Friday, August 07, 2015 12:57 AM
 To: gromacs.org_gmx-users@maillist.sys.kth.se
 Subject: [gmx-users] g_sham

 Dear All,
 I searched a lot more things about g_sham in the mailing list and
 eventually getting confused with the inputs. Just make me clear about:

 1. Is it feasible to obtain free energy landscape (FEL) from a 2D
 projection (using g_anaeig) of  index groups (say some loop's atoms) which
 are used for the least squares fit in g_covar and then selecting index
 group of elements that corresponds to the eigenvectors (say Prot-masses)?
 Or,
 Should I calculate covariance (g_covar) of my concerned loops separately
 and then should I go for g_sham?

 2. Is there any representative way to get the exact time point for the
 corresponding minima obtained from g_sham?


 Thanks for all previous helps...
 Naba

 Bioinformatics Infrastructure Facility
 Department of Animal Biotechnology
 College of Veterinary Science
 Khanapara,Guwahati 781022
 Assam, India
 --
 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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 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.




-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
Gromacs Users mailing list

Re: [gmx-users] sample working DNA file?

[Naba]

Try using xleap of AmberTools.
http://ambermd.org/tutorials/advanced/tutorial4/

On Wed, Aug 12, 2015 at 5:06 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 8/12/15 6:07 AM, toannt wrote:

 Hi all,

 I have problems with a simple setup of DNA system. I try some programs to
 generate DNA pdb file. Some pdb output doesn't work. Some requires a lot
 of
 manual edits. I finally got a pdb file working but I still have some
 problems
 with long bonds. Does anybody have a sample working DNA pdb file and
 could
 share with me?


 DNA structures unfortunately do not always have the same level of
 standardized nomenclature as proteins, so some manual editing or use of
 .r2b files is needed, especially as naming also varies among force fields.
 A sort of bulletproof DNA structure is PDB 1BNA (or really anything else
 that isn't missing any atoms).

 -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

 ==

 --
 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.




-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
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.

Re: [gmx-users] g_sham

[Naba]

Thank you very much Micholas.
I have actually done the second option. But I was uncertain whether I have
done are all nonsense.
From your replies it seems that I am quite close to fulfill my objectives.
Meanwhile, I am about to perform dPCA for those loops as you have suggested
in the previous mail.
Thanks a lot.

On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. smit...@ornl.gov
wrote:

 Hi Naba,

 I believe you would want to do your second option if you want to include
 the contributions from all of the loops. If you are just interested in one
 loop, then you would do each seperately. Rule-of-thumb for these
 calculations are whatever group you use for the convariance matrix, is what
 you should use for the 2D projection.

 Hope that helps.


 ===
 Micholas Dean Smith, PhD.
 Post-doctoral Research Associate
 University of Tennessee/Oak Ridge National Laboratory
 Center for Molecular Biophysics

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba 
 nabajyoti.gosw...@gmail.com
 Sent: Thursday, August 13, 2015 4:17 AM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] g_sham

 Thanks for the reply Micholas.

 I read the special discussion on dPCA at your provided link. But that is a
 fact of small peptide penta-alanine.
 I actually completed a 100 ns simulation of a outermembrane protein (of 239
 amino acid residues) with 284 DMPC molecules. The protein contains 4
 extracellular loops of variable lengths and I want to study the dynamics of
 these loops. What I wanted to confirm is:

 1. Is it all right if I extract covariance separately for each loops? OR,
 2. Should I calculate covariance of index groups of my concerned loops and
 then should I proceed to 2D projection (by g_anaeig)?


 On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. smit...@ornl.gov
 wrote:

  1. Is it feasible to obtain free energy landscape (FEL) from a 2D
  projection (using g_anaeig) of  index groups (say some loop's atoms)
 which
  are used for the least squares fit in g_covar and then selecting index
  group of elements that corresponds to the eigenvectors (say
 Prot-masses)?
  Or,
  Should I calculate covariance (g_covar) of my concerned loops separately
  and then should I go for g_sham?
 
  I am not sure if I understand, however, I think I may be able to help a
  litttle. g_sham is just a histograming program that inverts the resulting
  histogram into energy space, so using a 2D projection is a legitimate
 use.
  Indeed what you are trying to do is very similar to the steps used in
 dPCA
  (see:
 
 http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
  ).
 
  2. Is there any representative way to get the exact time point for the
  corresponding minima obtained from g_sham?
 
  If you have the time series for each of the coordinates used in the 2D
  projection you just need to scan through the 2D timeseries for values
 that
  match the minimia. e.g. If in the g_sham a minima is at coordinates
 (10,10)
  than you need to scan through the timeseries of your coordinates:
  time coord1 coord2
  1 00
  2 1   10
  3 40 400
  41025
  ...
  ...
  5000  10 10
  .
  6000   1010
  .
  988908   10  10
  
 
 
  where frames 988908, 5000, and 6000 are the ones you are looking for. You
  could extract these with
 
  awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline 
 
 yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==$y){print
  $1}}' yourfile_second_coordinate_here.xvg
 
  where you would provide the x and y coords of the minina where I have
  coord1min and coord2min.
 
  You may be more interested in getting frames near the minimia and not
  actually on it, in which case just change the last if-statement as
 needed.
 
  Hope that helps.
 
  -Micholas
 
  ===
  Micholas Dean Smith, PhD.
  Post-doctoral Research Associate
  University of Tennessee/Oak Ridge National Laboratory
  Center for Molecular Biophysics
 
  
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba 
  nabajyoti.gosw...@gmail.com
  Sent: Friday, August 07, 2015 12:57 AM
  To: gromacs.org_gmx-users@maillist.sys.kth.se
  Subject: [gmx-users] g_sham
 
  Dear All,
  I searched a lot more things about g_sham in the mailing list and
  eventually getting confused with the inputs. Just make me clear about:
 
  1. Is it feasible to obtain free energy landscape (FEL) from a 2D
  projection (using g_anaeig) of  index groups (say some loop's atoms)
 which
  are used for the least squares fit in g_covar and then selecting index
  group of elements that corresponds to the eigenvectors (say Prot-masses)?
  Or,
  Should I calculate

[gmx-users] g_sham

[Naba]

Dear All,
I searched a lot more things about g_sham in the mailing list and
eventually getting confused with the inputs. Just make me clear about:

1. Is it feasible to obtain free energy landscape (FEL) from a 2D
projection (using g_anaeig) of  index groups (say some loop's atoms) which
are used for the least squares fit in g_covar and then selecting index
group of elements that corresponds to the eigenvectors (say Prot-masses)?
Or,
Should I calculate covariance (g_covar) of my concerned loops separately
and then should I go for g_sham?

2. Is there any representative way to get the exact time point for the
corresponding minima obtained from g_sham?


Thanks for all previous helps...
Naba

Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
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.

[gmx-users] Regarding g_sham

[Naba]

Dear All,
I searched a lot more things about g_sham in the mailing list and
eventually getting confused with the inputs. Just make me clear about:

1. Is it feasible to obtain free energy landscape (FEL) from a 2D
projection (using g_anaeig) of  index groups (say some loop's atoms) which
are used for the least squares fit in g_covar and then selecting index
group of elements that corresponds to the eigenvectors (say Prot-masses)?
Or,
Should I calculate covariance (g_covar) of my concerned loops separately
and then should I go for g_sham?

2. Is there any representative way to get the exact time point for the
corresponding minima obtained from g_sham?


Thanks for all previous helps...
Naba




Nabajyoti Goswami

Department of Animal Biotechnology
College of Veterinary Science
Assam Agricultural University
Khanapara, Guwahati 781022
Assam, India
-- 
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.

[gmx-users] Regarding g_sham

[Naba]

Dear All,
I searched a lot more things about g_sham in the mailing list and
eventually getting confused with the inputs. Just make me clear about:

1. Is it feasible to obtain free energy landscape (FEL) from a 2D
projection (using g_anaeig) of  index groups (say some loop's atoms) which
are used for the least squares fit in g_covar and then selecting index
group of elements that corresponds to the eigenvectors (say Prot-masses)?
Or,
Should I calculate covariance (g_covar) of my concerned loops separately
and then should I go for g_sham?

2. Is there any representative way to get the exact time point for the
corresponding minima obtained from g_sham?


Thanks for all previous helps...
Naba




Nabajyoti Goswami

Department of Animal Biotechnology
College of Veterinary Science
Assam Agricultural University
Khanapara, Guwahati 781022
Assam, India
-- 
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.

Re: [gmx-users] ProDrg

[Naba]

How about ACPYPE for AMBER force field?

On Tue, Dec 9, 2014 at 12:56 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/8/14 2:12 PM, xy21hb wrote:

 Dear all,

 Since Justin mentioned in previous mails that PRODRG is almost unreliable,
 is there any reliable source for patching a new small molecule for
 gromacs, in general?


 When it comes to force fields, you can't speak in generalities.  Any new
 species must be parametrized in accordance with the methods of the parent
 force field, for balance and consistency.  The ATB server is significantly
 better than PRODRG for Gromos-compatible compounds.  There are other
 servers for other force fields (ParamChem for CHARMM/CGenFF, etc) but no
 black-box method should be trusted without scrutinizing and testing
 extensively.

 The bottom line is that parametrization of new species is hard, and it
 often requires significant effort in finding suitable target data, refining
 parameters to match, then validating that those parameters are actually
 useful in subsequent simulations.  This is common across all simulation
 codes and all force fields.

 -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

 ==

 --
 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.




-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
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.