[gmx-users] Question on energygrps setting

[Justin Lemkul]

On 5/7/20 10:49 AM, Devargya Chakraborty wrote:
> Suppose my system contains an anion a cation and water and I have done an
> nvt simulation.after the completion I want to see the energy profile of the
> individual groups like the cation or the anion etc. Can anybody guide me
> how to use the energy grps option in analysing that.

You wouldn't. The energygrps setting is specifically for computing 
interaction energies between two groups. It cannot be used to give you 
the energy of a group.

You could do that by extracting coordinates of interest from the 
trajectory with trjconv, making a matching .tpr with convert-tpr, and 
then using mdrun -rerun to recompute the energies. While you *can* do 
this, note that these values will generally have no physical meaning.

-Justin

> Thanks
> Devargya Chakraborty
>
> On Thu 7 May, 2020, 5:48 PM Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 5/6/20 6:31 PM, Lei Qian wrote:
>>> Dear users,
>>>
>>> I know interaction energy calculation is carried out via energygrps
>> setting
>>> in mdp file.
>>> Because free energy-related settings do not include this energygrps
>>> setting, so I think this energygrps setting may NOT be related to free
>>> energy settings.
>>> Could I ask whether my idea is correct or not?
>> The two have nothing to do with one another. In general, energygrps
>> shouldn't be used during an MD simulation anyway, and should be treated
>> as an analysis method.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> 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-request at gromacs.org.
>>

-- 
==================================================

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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================