[gmx-users] Question on energygrps setting
jalemkul at vt.edu
Thu May 7 16:52:57 CEST 2020
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.
> 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
>>> 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 A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
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>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
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>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
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
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