Re: [gmx-users] (no subject)
On 9/14/13 7:31 AM, mabbasi wrote: Dear All users I used OPLS ff for my system. After md production I get this error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- == Justin A. Lemkul, Ph.D. 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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] (no subject)
Dear All users I used OPLS ff for my system. After md production I get this error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated. maryam abbasi, PhD student of Medicinal Chemistry Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences (http;//pharm.mui.ac.ir/) Isfahan University of Medical Sciences (http://www.mui.ac.ir), Hezar Jerib Ave. Isfahan, I.R.IRAN -- gmx-users mailing listgmx-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
Re: [gmx-users] Distance calculation
g_mindist also has something useful in this direction, I guess. Dr. Vitaly V. Chaban On Sat, Sep 14, 2013 at 12:10 AM, Rama wrote: > > Hi , > > I there any tool to calculate distance between particular atom from one > group(protein) to particular atom from another group(DMPC lipid in > Bilayer). > For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in > DMPC lipid. > > Thanks > Rama > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Distance-calculation-tp5011170.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-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 listgmx-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
