Hi gromacs users, I am trying to run coarse-grained MD for a protein system using martini protocol. First step is to run short min in vacuum, whenever I try to do this I am getting an error regarding my input file.
ERROR 1 [file system-vaccum.top, line 16]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "I Caught It In the Face" (P.J. Harvey) My input file: integrator = steep dt = 0.02 nsteps = 10 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout = 100 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein tau-t = 1.0 ref-t = 300 How should I modify it? Thank you in advance for any suggestions. best regards Urszula ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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.
