[gmx-users] lennard-jones 9-3 wall ( Gromacs & LAMMPS )

[SaeeD PourasaD]

Dear Gromacs users ,

​I have a question about Lj Wall 9-3 in Gromacs and LAMMPS !
​in Gromacs this is the definition of wall : L J integrated over the volume
behind the wall: 9-3 potential .
In LAMMPS there is no any special definition for that .
Can you please let me know what the difference is between these two walls
in Gromacs and LAMMPS ?

Regards,
Saeed.

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Phone : +82-52-217-5629
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Re: [gmx-users] Md simulation trajectory Analysis.

[Mark Abraham]

Hi,

On Mon, 14 Nov 2016 07:14 maria khan  wrote:

Dear Justin Lemkul..
Analysing trajectories of Md simulation,,how the H-bonds can be
analysed..if after minimization the software has once ignored the
H-bonds..??


Typical force fields don't explicitly model hydrogen bonds, but that
doesn't mean the underlying physics is ignored. "Analyse the h-bonds" is a
bit vague. What did you design the simulation to observe?

Secondly how can we rename the H atoms by the gromacs conventional
system.Guide me in renaming H atoms of His residue according to conventions?


Why do you think you need to?

Mark

Maria khan
regards and thank.
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[gmx-users] Md simulation trajectory Analysis.

[maria khan]

Dear Justin Lemkul..
Analysing trajectories of Md simulation,,how the H-bonds can be
analysed..if after minimization the software has once ignored the
H-bonds..??
Secondly how can we rename the H atoms by the gromacs conventional
system.Guide me in renaming H atoms of His residue according to conventions?
Maria khan
regards and thank.
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Re: [gmx-users] REMD ensemble of states

[Abramyan, Tigran]

Thank you Mark,

One more question regarding the centering of the frames at 300 replica (0.xtc) 
using trjconv. I have used a few trjconv options, however do not seem to be 
removing jumps from the original trajectory. For example, the command below 
works for me when applied to the *xtc file produced in regular MD, however, 
with REMD it produces a trajectory which won't be of use for example in VMD:

 echo 1 | trjconv -s 0.tpr -f 0.xtc -o 300.xtc -pbc nojump -dt 40

I am assuming I may need to use a combination of tpr files to produce the 
nojump 300.xtc file?

Please advise,
Thank you very much.
Tigran



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Tuesday, November 8, 2016 1:15 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD ensemble of states

Yes

On Tue, 8 Nov 2016 18:43 Abramyan, Tigran  wrote:

> Hi Mark,
>
> Thanks a lot for your prompt response. So  demux.pl creates continuous
> trajectories, *_trajout.xtc, but the ensemble of states (lowest energy
> ensemble, typically of interest in the analysis of REMD results) is saved
> in the original  0.xtc file produced during REMD before using demux.pl?
>
> Thank you,
> Tigran
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Tuesday, November 8, 2016 5:53 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REMD ensemble of states
>
> Hi,
>
> Mdrun wrote that. You made the trajectories contiguous with the demux.
>
> Mark
>
> On Tue, 8 Nov 2016 04:55 Abramyan, Tigran  wrote:
>
> > Hi,
> >
> >
> > I conducted REMD, and extracted the trajectories via
> > trjcat -f *.trr -demux replica_index.xvg
> > And now I was wondering which *.xtc file is the ensemble of states at the
> > baseline replica (lowest temperature replica). Intuitively my guess is
> that
> > the numbers in the names of *_trajout.xtc files correspond to the replica
> > numbers starting from the baseline, and hence 0_trajout.xtc is the
> ensemble
> > of states at the baseline replica, but I may be wrong.
> >
> >
> > Please suggest.
> >
> >
> > Thank you,
> >
> > Tigran
> >
> >
> > --
> > Tigran M. Abramyan, Ph.D.
> > Postdoctoral Fellow, Computational Biophysics & Molecular Design
> > Center for Integrative Chemical Biology and Drug Discovery
> > Eshelman School of Pharmacy
> > University of North Carolina at Chapel Hill
> > Chapel Hill, NC 27599-7363
> >
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Re: [gmx-users] gmx do_dssp

[Mark Abraham]

Hi,

That depends what they've changed. We haven't changed things in years.

Mark

On Sun, 13 Nov 2016 15:43  wrote:

> Hello,
> Does the gmx do_dssp command works with dssp version 2.2.1 ?
>
> Regards,
> Amit
>
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[gmx-users] gmx do_dssp

[amitbehra]

Hello,
Does the gmx do_dssp command works with dssp version 2.2.1 ?

Regards,
Amit

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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Hi all,

I tried to estimate the free energy of betaine on betaine covered surface. My 
target molecule is also on the surface.
In order to do that I turn off charges linearly, then turn off LJ with a 
sort-core potential. 
Lambda is increased with 0.1 intervals for coulombic part and 0.05 intervals 
for LJ.
I did NVT simulation and I applied a flat-bottom potential on surface molecules.
However the result seems a little bit strange, first I could not see any minima 
in free energy from lambda 0 to 1 (I assume there should be minima aroma 
lambda=0.6-0.7). 
Also my histogram plot also seems strange that I have very big numbers on x 
axis (like e+33).
Please see the plots link below.

https://imgur.com/a/fqgmi

Any help would be appreciated.
Thanks.
> On 06 Nov 2016, at 14:33, Justin Lemkul  wrote:
> 
> 
> 
> On 11/6/16 8:27 AM, gozde ergin wrote:
>> 
>>> If it's the salt, then take the known Na+ value for the force field and add 
>>> it to the SDS value you obtain at infinite dilution. Straightforward.
>> 
>> Ok either I can take hydration free energy of Na from the literature or I 
>> can run 2 thermodynamic integration with dodecyl sulfate and Na separately 
>> and sum them.
>> 
> 
> Yes, because DeltaG is a state function.
> 
>> Besides this I would like ask how did you manage the get the very similar 
>> solvation free energy result with experiments without adding Coulomb 
>> interaction which means decoupling only the L-J?
> 
> The reference quantity is just the LJ component of the total free energy; 
> please see the referenced paper by Shirts et al.  Methane is net-neutral and 
> the LJ will dominate, anyway, but the quantity shown (and explicitly stated) 
> is NOT the hydration free energy, just part of it.
> 
>> Do you think to estimate the correct solvation free energy for dodecyl 
>> sufate(-) and Na(+) I need to decouple also the Coulombic interaction?
> 
> Of course, those will be critical for charged species.
> 
>> If yes, in order to do that I just need to modify the coul_lambdas parameter 
>> in .mdp file, right?
> 
> Yes.
> 
>> Also I should not make the charge of the atoms as zero in topology file.
> 
> Correct.
> 
>> According to the Sander Pronk tutorial of Solvation free energy of ethanol, 
>> I can turn off both the electrostatic (Coulomb) interactions and the Van der 
>> Waals (Lennard-Jones) interactions at the same time.
>> 
> 
> This may be unstable, and is generally not done.  Turn off charges linearly, 
> then turn off LJ with a soft-core potential (or vice versa).  The point is 
> you should never have charges on atoms with no (or drastically reduced) LJ 
> terms. This can be easily specified in an appropriate series of lambda states 
> in the .mdp file.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
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Re: [gmx-users] Umbrella Sampling

[gozde ergin]

Hey,

Did you change the number inside the distances.pl script?
If you have 1000 files, you need to change the number of 500 on line 6, 13 , 
and  36 (lines start with for loop) make them 1000.
> On 13 Nov 2016, at 11:10, Mouri Ahmed  wrote:
> 
> Hi everyone,
> 
> I have run pulling simulation for the protein complex system. I have got
> 1000 configuration files. And in the summary_distances.dat, I have found
> 0-500 distances.
> 
> How will I select configuration file for the npt_umbrella simulation.
> 
> Thanks in advance. I will be very grateful for the help.
> 
> Best Regards
> Mouri
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[gmx-users] Umbrella Sampling

[Mouri Ahmed]

Hi everyone,

I have run pulling simulation for the protein complex system. I have got
1000 configuration files. And in the summary_distances.dat, I have found
0-500 distances.

How will I select configuration file for the npt_umbrella simulation.

Thanks in advance. I will be very grateful for the help.

Best Regards
Mouri
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