2015-08-25 17:29 GMT-03:00 David van der Spoel <sp...@xray.bmc.uu.se>:
> On 25/08/15 18:24, Marcelo Depólo wrote: > >> Hi all! >> >> I've been running gmx dos (version 5.0.4) in some trajectories with the >> following: >> >> echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos >> dos.xvg -vacf vacf.xvg -mvacf mvacf.xvg >> >> and it runs just fine. But when I run the same line with 5.0.6, I get: >> >> That means the results from previous versions may not have been what you > thought they would be. What are you trying to accomplish? gmx dos does not > do anything useful with an index file. > I am calculating Cv from DoS simulations. Still, I haven't use any index file in my line. I used precisely the same one as above. I have checked both gmx_dos.c and there is a new code implemented on 5.0.6, exactly in the part of counting atoms (if I am not mistaken). > >> >> >> >> >> *-------------------------------------------------------Program gmx_506, >> VERSION 5.0.6Source code file: >> >> /home/marcelodepolo/Downloads/BACKUP-softwares/gromacs-5.0.6/src/gromacs/gmxana/gmx_dos.c, >> line: 93Fatal error:Index contains atom numbers larger than the topology* >> >> Did anyone already come across this? >> >> Cheers! >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > 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. -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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.