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, <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 > >> > >> -- > >> ================================================== > >> > >> 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 > >> > >> ================================================== > >> > >> -- > >> 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-requ...@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 > > jalem...@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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
