Dear Justin, I am following membrane-protein tutorial to construct my system. During equilibration and production MD, I am receiving the following NOTES.
NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 I have downloaded the mdp files from tutorial. Is it ok if I omit these notes and carry the production run? On Tue, Jun 10, 2014 at 5:41 PM, Justin Lemkul <[email protected]> wrote: > > > On 6/10/14, 1:12 AM, Venkat Reddy wrote: > >> I have used >> editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro >> to set the box. >> >> Then >> genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro >> got hanged >> >> >> Am I missing something here??? >> > > Don't extend the z-dimension at this stage. You want to expand the > membrane laterally (along x and y, usually), so set the box vectors > manually with editconf -box, not -d (though using -d can tell you what > suitable vectors in x and y might be). You can always increase the > z-dimension, if you need to, later using editconf and then fill with water > using genbox in a separate step. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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].
