Thank Tsjerk so much ! But after being minimized 50000 steps and equilibrated 90 ns, there are some bonds in the system that rotate more than 30 degrees. I applied tips for blew up system as you advised. But the system does not achieve balance. Should i carry out more many steps for minimization ? or minimize many times ? to get more equilibrated system.
Regards, KT On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > Hi KT, > > This is caused by another problem. Your system blew up. Check messages > before this one, and check the log for LINCS warnings. > > Cheers, > > Tsjerk > > On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com > >wrote: > > > Dear All, > > > > My MD simulation has an error > > > > Warning: Only triclinic boxes with the first vector parallel to the > x-axis > > and the second vector in the xy-plane are supported. > > Box (3x3): > > Box[ 0]={ nan, nan, nan} > > Box[ 1]={ nan, nan, nan} > > Box[ 2]={ nan, nan, nan} > > Can not fix pbc. > > > > I searched on Gromacs-errors web, but i did not see this error. > > How can i fix it ? > > > > Thanks and regards, > > KT > > -- > > gmx-users mailing list gmx-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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > gmx-users mailing list gmx-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 list gmx-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