[gmx-users] Output forces only for select group of atoms

[Jacob Alan Spooner]

Hi Mark,

Thank you for your speedy reply.  Unfortunately I do not think a rerun will solve my problem since in that case I will just have to output coordinates of the entire system at my desired output frequency for the forces, and will still be generating huge trajectory files.  Ideally I would be outputting the coordinates of the entire system very very infrequently (since I am not really interested in the coordinates), and outputting the forces for a small group of atoms very frequently. So in this case I don't think doing a rerun will save me anyting and will just add a post-processing step. Normally this would not be an issue but I will be running many simulations of these 250000 atom systems at once, so outputting all the forces (or coordinates) when I only care about a fraction of them will be a significant problem.

If anybody else has any ideas about how I could get around this issue I would be thankful, but I suspect there is no simple solution.

Best,
Jake
 
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: Tuesday, February 27, 2018 1:47 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Output forces only for select group of atoms

Hi,

No, but instead see
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation

Mark

On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner <Jacob.Spooner at ufv.ca>
wrote:

> Dear GROMACS users,
>
> I am simulating a fairly large system of about 250000 atoms and I want to
> analyze the forces at each output step for only a select group of about 200
> atoms (and actually only the z component of the force but this is less
> important).  My question is whether or not there is a simple way to
> selectively output forces for only my atoms of interest.  I will have long
> runs and high output frequency so I would really like to avoid having to
> output force data for the other ~249800 atoms in my system.  Any help is
> greatly appreciated!
>
> Thanks,
> Jake Spooner
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