Hi, You haven't done a simulation, you've moved down a potential energy surface from one point to another. Of course the potential energy deviates. How much depends how far away from something reasonable you were when you started :-)
Mark On Sun, Mar 19, 2017 at 2:19 AM Mishelle Oña <samimi...@hotmail.com> wrote: > Thanks for your answer Justin. > > Another question for the same simulation. I got this values of potential > energy: > > Average> -127776 > > Err.Est.>4900 > > RMSD>12891.3 > > Tot-Drift> -32877.9 > > I think the RMSD is way too high. What do you think? > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin > Lemkul <jalem...@vt.edu> > Sent: Saturday, March 18, 2017 8:06 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Pressure problem in EM simulation > > > > On 3/18/17 9:00 PM, Mishelle Oña wrote: > > Hello! > > > > I have a question about pressure in EM simulation. I am using Steepest > descent method in a water polymer system. My pressure gets this value: > > > > Energy Average Err.Est. RMSD Tot-Drift > > > ------------------------------------------------------------------------------- > > Pressure -2843.38 65 162.655 -446.059 > (bar) > > > > The pressure value is very weird. Is this normal? or I am doing > something wrong? > > > > There's no barostat or velocities during EM so the value you see has no > real > significance. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]< > http://mackerell.umaryland.edu/~jalemkul> > > Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul> > mackerell.umaryland.edu > Welcome to my site! To learn more about me and the work I am doing, please > use the navigation links above. > > > > ================================================== > -- > 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. > -- 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.
