Hi, Following were the commands which i used in the umbrella sampling simulations:
grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr mdrun -v -deffnm umbrella500 Output: umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log, umbrella500.gro, umbrella500.edr, umbrella500.cpt pullf.xvg and pullx.xvg files were not produced. Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the mdrun? Kind regards, chetan ________________________________________ From: [email protected] [[email protected]] On Behalf Of [email protected] [[email protected]] Sent: 15 December 2010 17:00 To: [email protected] Subject: [gmx-users] pullx.xvg / pullf.xvg please copy and paste your commands your output. It is unlikely that any of us are going to do that tutorial in order to understand your question. -- original message -- Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella sampling simulations, but for each configuration it outputted a single xvg file. For the data analysis i should have pullf.xvg / pullx.xvg files....but these files are not outputted after the simulation run. I haven't made any changes to the .mdp files mentioned in the tutorial. Please can i know what might have gone wrong that it has not produced pullf.xvg and pullx.xvg files. Kind regards, chetan. -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
