I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more ns ?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Sunday, January 6, 2013 9:15 AM Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory On 1/6/13 12:33 AM, Shima Arasteh wrote: > Do you mean that I re-run NPT step with the new index file and npt.gro (which > I got from the last NPT equilibration)? That's not clear to me yet. > That's where I'd start. You may have to run the new configuration through the entire equilibration protocol, though. Instability during MD often indicates inadequate equilibration, so whatever your protocol is may not be sufficient as is and may require greater time. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
