[gmx-users] Question on energygrps setting

[Devargya Chakraborty]

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.

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
>
> ==================================================
>
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> Gromacs Users mailing list
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