Hi, I also tried the energy minimization but it seems not to work. In fact, when I run a similar case like this(just including some DNA single strand) ,it is going on well but after I increase some more single DNA strand to the system it just show such error.
Yang ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel [sp...@xray.bmc.uu.se] Sent: Sunday, April 26, 2009 12:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] XTC.error He, Yang wrote: > Hi all users, > > When I run the mdrun command, it always shows that XTC.error. Then I check > the md.log file and find that: > > There are 220 atoms in your xtc output selection 220 atoms and 3.9e5 bond energy: that is roughly 2000 kJ/mol per bond, indicating that bonds on average have been elongated by 1 angstrom. Seems your structure is not good... Try minimizing. And note that gromacs uses nm, in case you have generated your own input... > Energies (kJ/mol) > Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR) > 3.91620e+05 9.58742e+03 1.93313e+04 -1.12241e+01 0.00000e+00 > Potential Kinetic En. Total Energy Temperature Pressure (bar) > 4.20528e+05 nan nan nan 0.00000e+00 > > ------------------------------------------------------- > Program mdrun, VERSION 3.3.1 > Source code file: stat.c, line: 257 > > Fatal error: > XTC error > > The total energy is shown"nan" I also checked my gro file but there are no > lapped atoms. And when I run the command "grompp", there is no any warnings. > > Can anybody tell me what is the problem about this error? > > Thank you very much. > > Yang > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php