[gmx-users] Question on energygrps setting

[Justin Lemkul]

On 5/7/20 10:57 AM, Devargya Chakraborty wrote:
> I think I couldn't frame the question correctly. Let's say I have a silica
> surface and I have water droplet on it and after a proper nvt simulation I
> want to calculate the interaction energy of the water droplet with the
> surface then how can I use the energy grps option for analysis.

You would specify groups (with an index file or from default groups) e.g.

energygrps = SOL Surface

-Justin

> Thanks
> Devargya Chakraborty
>
> On Thu 7 May, 2020, 8:23 PM Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>>>
>>>> ==================================================
>>>>
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>> --
>> ==================================================
>>
>> 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
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>> * Please search the archive at
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-- 
==================================================

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

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