Dear Tsjerk, Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong. I am looking forward to getting a reply from you. Brett
At 2015-04-26 20:59:59, "Tsjerk Wassenaar" <[email protected]> wrote: >Hi Brett, > >Too high for what? > >You do EM because you just built (part of) your system, and in doing so >introduced clashes and non-ideal geometries. These lead to high potential >energy, so you relax them with EM. What you see is how much the system >relaxed. Noone usually cares how much potential energy was lost during EM. >The thing that matters is whether the resulting system is relaxed enough to >run the simulation. > >Cheers, > >Tsjerk > >On Sun, Apr 26, 2015 at 2:43 PM, Brett <[email protected]> wrote: > >> Dear All, >> >> I just run the command gmx energy -f em.edr -o potential.xvg for my energy >> minimization step MD, but I find the RMSD given by this command is 142611, >> which I regard to be too high. >> >> Will you please explain to me what leads to the so high RMSD (Err.Est is >> 53000, Tot-Drift is -341107 KJ/mol)? >> >> I am looking forward to getting your reply. >> >> Brett >> -- >> 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 [email protected]. >> > > > >-- >Tsjerk A. Wassenaar, Ph.D. >-- >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 [email protected]. -- 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 [email protected].
