Re: [gmx-users] Question on energygrps setting
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, 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, 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. -- == 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.
Re: [gmx-users] Question on energygrps setting
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, 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, 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.
Re: [gmx-users] Question on energygrps setting
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, 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.
Re: [gmx-users] Question on energygrps setting
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. Thanks Devargya Chakraborty On Thu 7 May, 2020, 5:48 PM Justin Lemkul, 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. > -- 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.
Re: [gmx-users] Question on energygrps setting
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.
