Re: [gmx-users] calculating pairwise interactions
Changing these parameters is not good, you may need to refer the forcefield original articles. -- 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] calculating pairwise interactions
On 4/15/18 7:23 AM, Mark Abraham wrote: Hi, You can use energy groups in a tpr for a rerun, but you will not get any long-range contribution. Neither does any force field that I know of produce a useful quantity from such a calculation. Again, I'll bang the drum a little bit for CHARMM here - we do explicitly target QM interaction energies with (at least) water, therefore providing a standard of reference for all interaction energies. There are other cases in which we balance against additional interactions on the QM level. It's the only force field I know of that explicitly does this (most others either compute charges in a continuum model or just go straight for DGsolv). Decomposing LJ vs. Coulomb within the short-range nonbonded interaction energy is still totally useless, but I would argue that the total interaction energy can be meaningful, at least with CHARMM. -Justin Mark On Sun, Apr 15, 2018, 06:46 Sahithya S Iyer wrote: Hi gmx users, Can anyone please tell me how to get the values for pairwise interactions from a gromacs trajectory. I would like to get the pairwise energy interaction values (van der waal and electrostatics) for each pair. Thanks in advance, Sahithya. -- 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 Virginia Tech Department of Biochemistry 303 Engel Hall 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] calculating pairwise interactions
Thanks Mark ! By long range interactions value do you mean those beyond rvdw and rcoulomb ? Can I increase these cut-off and get some more interactions ? On Sun, Apr 15, 2018 at 4:53 PM, Mark Abraham wrote: > Hi, > > You can use energy groups in a tpr for a rerun, but you will not get any > long-range contribution. Neither does any force field that I know of > produce a useful quantity from such a calculation. > > Mark > > On Sun, Apr 15, 2018, 06:46 Sahithya S Iyer wrote: > > > Hi gmx users, > > > > Can anyone please tell me how to get the values for pairwise interactions > > from a gromacs trajectory. I would like to get the pairwise energy > > interaction values (van der waal and electrostatics) for each pair. > > > > Thanks in advance, > > > > Sahithya. > > -- > > 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. > -- 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] calculating pairwise interactions
Hi, You can use energy groups in a tpr for a rerun, but you will not get any long-range contribution. Neither does any force field that I know of produce a useful quantity from such a calculation. Mark On Sun, Apr 15, 2018, 06:46 Sahithya S Iyer wrote: > Hi gmx users, > > Can anyone please tell me how to get the values for pairwise interactions > from a gromacs trajectory. I would like to get the pairwise energy > interaction values (van der waal and electrostatics) for each pair. > > Thanks in advance, > > Sahithya. > -- > 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.
[gmx-users] calculating pairwise interactions
Hi gmx users, Can anyone please tell me how to get the values for pairwise interactions from a gromacs trajectory. I would like to get the pairwise energy interaction values (van der waal and electrostatics) for each pair. Thanks in advance, Sahithya. -- 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.
