Thanks.
You have mentioned "proper energy groups" in mdp file Could you please say more about it? Thanks, Kulkarni.R ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Vytautas Rakeviius <vytautas1...@yahoo.com> Sent: Thursday, March 16, 2017 10:29 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] LINEAR INTERACTION ENERGY Basically you do two MD runs one with ligand in water other with ligand in protein. You must set proper energygrps in mdp file so you get 2 edr files from runs and in the end you use "gmx lie" (http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between those two edr files.You might check this paper too: gmx lie - GROMACS<http://manual.gromacs.org/programs/gmx-lie.html> manual.gromacs.org Synopsis gmx lie [-f [.edr>]] [-o [.xvg>]] [-nice ] [-b ] [-e ] [-dt ] [-[no]w] [-xvg ] [-Elj ] [-Eqq ] [-Clj ] [-Cqq ] [-ligand ] Curr Comput Aided Drug Des. 2015;11(3):237-44. On Thursday, March 16, 2017 12:15 PM, Kulkarni R <alumniphys...@hotmail.com> wrote: Hi gromacs users, In order to calculate delta G (Gibbs free energy) for protein ligand binding, what are the steps to be followed in Linear interaction energy? Are there any tutorials for the same? Thanks, Kulkarni.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- 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.
