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, <jalem...@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, <jalem...@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

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Lab: 303 Engel Hall

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Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Blacksburg, VA 24061

jalem...@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

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

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

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