[gmx-users] How to calculate potential energy with dynamics selection index?

[Justin Lemkul]

On 12/6/19 2:06 PM, Peiyin Lee wrote:
> Hi, Alessandra,
>
>     Thank you for the reply. I have used the command "gmx_mpi select -f
> md.xtc  -s md.tpr  -n index.ndx  -select "(resname N2C6H11) and (within 0.5
> of group Protein)" -on" and it worked, but my problem is with the dynamics
> selection. As mentioned in the previous mail, this command will produced a
> massive number of indexes for every frame, and those indexes will be
> treated as static selection, not dynamics when doing rerun for the selected
> energy groups. I wonder if there is a way that I can compute the potential
> energy with dynamics selection (xx within some distance of yy). Thank you!

The only way to deal with selections of different sizes is to analyze 
each frame individually as a coordinate file, with a new .tpr file each 
time. It is not something that mdrun can handle automatically AFAIK.

-Justin

> Regards,
> Peiyin
>
> On Fri, Dec 6, 2019 at 8:24 AM Alessandra Villa <
> alessandra.villa.biosim at gmail.com> wrote:
>
>> Hi
>>
>> On Fri, Dec 6, 2019 at 5:36 AM Peiyin Lee <peiyinlee329 at gmail.com> wrote:
>>
>>> Dear users,
>>>
>>>     I am trying to calculate the VDW potential energy and electrostatic
>>> energy for solvent in the first solvation shell and in bulk for my
>>> simulation systems. In order to calculate the potential for solvent in
>> the
>>> FSS, I have to do gmx_energy with dynamics selection and do a rerun.
>>> However, gmx_make_ndx only supports static selection. I have also tried
>>> gmx_select, but this command gave me selections like "xx within 0.5 of
>> yy"
>>> for every frame and produced a massive amounts of indexes. Each index
>> seems
>>> to be treated as static index when I did a rerun and calculated
>> gmx_energy,
>>> which is not what I expected.
>> Does anyone know any way to perform
>>> dynamics selection? Thank you in advance!
>>>
>>>
>> Concerning the selection of the first hydration shell, try the following
>> command
>>
>> gmx select -f *.xtc -s *.tpr -select 'group SOL and same residue as within
>> VALUE of resname Y' -oi
>>
>> "VALUE" is  reference specific.
>>
>> Best regards
>> Alessandra
>>
>> Regards,
>>> Peiyin
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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