Hi Justin For now I used
*mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord <jjamesgreen...@gmail.com> wrote: > Hi Justin, > I have asked this before, but this time I started up from scratch and used > the input files that I know they are fine but again I am getting this > error, Would you please tell me what is wrong in my topology files and > where about in .top files the bond length are defined? > > > https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing > > Cheers > James > > On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/16/15 11:35 PM, James Lord wrote: >> >>> Hi Justin >>> Thanks for this. Can you tell me which step(s) this bond length is >>> defined???? >>> What should I do (redo) to resolve this issue? >>> >> >> The bonds are defined in the topology. The DD algorithm reads what's in >> the coordinate file and builds cells based on the geometry it finds there. >> >> Without a full description of what's in your system, what steps you've >> taken to prepare it (full commands, in order), there's little I can suggest >> because it would all be guesswork. >> >> >> -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 >> >> ================================================== >> -- >> 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.