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

[Justin Lemkul]

On 2/27/18 6:16 PM, Jacob Alan Spooner wrote:
> 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.

Short of modifying the code, the only option is what Mark suggested. 
GROMACS isn't designed to do what you're asking.

-Justin

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

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