RE: [gmx-users] pullx.xvg / pullf.xvg
Hi Carsten, Thank you very much. I reran my files: grompp -f md_umbrella.mdp -c conf144.gro -p topol.top -n index.ndx -o 144.tpr mdrun -s 144.tpr -rerun umbrella144.xtc -e 144.edr -o 144.trr -pf pullf.xvg -px pullx.xvg Output: 144.tpr, 144.trr, 144.edr, pullx.xvg, pullf.xvg. Kind regards, chetan. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Carsten Kutzner [ckut...@gwdg.de] Sent: 16 December 2010 14:28 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pullx.xvg / pullf.xvg On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote: > 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. With -deffnm you specified a default filename for all output files. Try to use mdrun -pf pullf.xvg -px pullx.xvg -s input.tpr Adding -h to mdrun will show you how your output files will be called. Carsten > > > Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the > mdrun? > > > Kind regards, > chetan > > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] > Sent: 15 December 2010 17:00 > To: gmx-users@gromacs.org > 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 filesbut > 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 listgmx-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 > > > > 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] pullx.xvg / pullf.xvg
On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote: > 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. With -deffnm you specified a default filename for all output files. Try to use mdrun -pf pullf.xvg -px pullx.xvg -s input.tpr Adding -h to mdrun will show you how your output files will be called. Carsten > > > Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the > mdrun? > > > Kind regards, > chetan > > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] > Sent: 15 December 2010 17:00 > To: gmx-users@gromacs.org > 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 filesbut > 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 listgmx-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 > > > > 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 listgmx-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 listgmx-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
RE: [gmx-users] pullx.xvg / pullf.xvg
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: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: 15 December 2010 17:00 To: gmx-users@gromacs.org 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 filesbut 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 listgmx-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 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 listgmx-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] 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 filesbut 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 listgmx-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] pullx.xvg / pullf.xvg
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 filesbut 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. 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 listgmx-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
