Thanks Justin for all your Help, i´m going to do all you suggesta and prepare a new structure, but before that i would like to try with a POSRE for the protein 10000 due to i am using 1000, also i would like to tell you, that due to the channel , is too big, in order to embebed in a 512 POPC Box, i deleted some residues located at the terminal (inside the membrane) , so i think this could be one reasson of the problem.
Thanks again, Thanks Andres Ortega > Date: Sat, 15 Mar 2014 18:04:07 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] NVT problem > > > > On 3/15/14, 5:29 PM, Andres Ortega Guerrero wrote: > > Hi Justin, > > > > I have done a 1ns MD with DOX + water + CL ion , the topology didn´t > > present any problem, > > > > i also did what you suggested, a -DFLEXIBLE EM and settle EM, but when i > > was trying to do my nvt.mdp > > > > Step 0, time 0 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 0.003859, max 0.176655 (between atoms 47397 and 47398) > > bonds that rotated more than 30 degrees: > > > > WARNING: Listed nonbonded interaction between particles 7156 and 7175 > > at distance 3f which is larger than the table limit 3f nm. > > > > IMPORTANT: This should not happen in a stable simulation, so there is > > probably something wrong with your system. Only change the table-extension > > distance in the mdp file if you are really sure that is the reason. > > > > this are the warning that appear, so based on this, the main problem seems > > like to be my structure right? > > maybe, the DOX is misplaced or something like that, so should i prepare > > again the .gro files? > > > > Yes, if the simulation crashes at step 0 there are severe problems with the > structure. The error messages tell you the problematic atoms, so simple > visualization should tell you what is going on. > > -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]. -- 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].
