Hi! I am currently working on another issue with the GB-double precision loops. I'll include this as well. But your pdb-file only contains 1 residue with the name UNK (by openBabel). Could you please send me another pdb-file that reproduces this error off-list, and I'll get to it.
Cheers /Per 7 sep 2010 kl. 09.59 skrev Silvio a Beccara: > Dear friends, > > when trying to run a double precision vanilla MD, version 4.5.1, with a small > hairpin molecule (248 atoms) in implicit solvent (generalized Born > approximation) this is what I get: > > --------------------------------------------------------------------------------------------- > Getting Loaded... > Reading file hairpin-md-gb-1.tpr, VERSION 4.5.1 (double precision) > Loaded with Money > > starting mdrun 'Protein' > 50000 steps, 50.0 ps. > Segmentation fault > --------------------------------------------------------------------------------------------- > > In some trials, I also get a message about the distance in an 1-4 interaction > being beyond the table size, but this is not the case. > > Strangely enough, the MD runs fine with a development version (4.0.99, > downloaded from the GIT repository). > > I am attaching my mdp and pdb files. > > > Regards > > > Silvio a Beccara > > > Dip. di Fisica - Universita` di Trento > 14 Via Sommarive > 38123 Povo - TN > tel: 0461-881631 > <md-gb.mdp><ratch-frame63.pdb>-- > 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