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 <brettliu...@163.com> 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
