Re: [gmx-users] problem with mdrun performing replica exchange MD
On Fri, 23 Nov 2007 12:42:45 +0100 "Xavier Periole" <[EMAIL PROTECTED]> wrote: David is write, you need to rename the tpr files is the following cmd: well, I believe David was right not write :)) mpirun -np 8 mdrun_mpi -s XXX.tpr -replex 2500 -reseed -1 -multi 8 by XXX0.tpr XXX1.ptr ... XXX7.tpr This time I used the following command line: mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8. I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul0_md0.tpr --- "Don't Eat That Yellow Snow" (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8. I could not understand this error because I do not have such a file: simul0_md0.tpr. -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:44:47 +0200 Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] problem with mdrun performing replica exchange MD >Date: Fri, 23 Nov 2007 11:30:53 +0200 > >Hi All, > >I am performing replica exchange molecular dynamics simulation(REMD). I >have 16 replicas each of which has a peptide with different conformation. >After obtaining .tpr files (at desired temperatures) for each replicas, I >loaded them via mdrun, but I got the following error: > >Fatal error: >Nothing to exchange with only one replica >--- > >Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The
Re: [gmx-users] problem with mdrun performing replica exchange MD
David is write, you need to rename the tpr files is the following cmd: mpirun -np 8 mdrun_mpi -s XXX.tpr -replex 2500 -reseed -1 -multi 8 by XXX0.tpr XXX1.ptr ... XXX7.tpr This time I used the following command line: mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8. I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul0_md0.tpr --- "Don't Eat That Yellow Snow" (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8. I could not understand this error because I do not have such a file: simul0_md0.tpr. -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:44:47 +0200 Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] problem with mdrun performing replica exchange MD >Date: Fri, 23 Nov 2007 11:30:53 +0200 > >Hi All, > >I am performing replica exchange molecular dynamics simulation(REMD). I >have 16 replicas each of which has a peptide with different conformation. >After obtaining .tpr files (at desired temperatures) for each replicas, I >loaded them via mdrun, but I got the following error: > >Fatal error: >Nothing to exchange with only one replica >--- > >Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - _
Re: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
This time I used the following command line: mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8. I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul0_md0.tpr --- "Don't Eat That Yellow Snow" (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8. I could not understand this error because I do not have such a file: simul0_md0.tpr. -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange >MD >Date: Fri, 23 Nov 2007 11:44:47 +0200 > >Hi Berk, > >I indicated the number of replicas with -multi option. In additon, I have >compiled Gromacs with MPI support. > >I used the following command line: > >mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 > >-Original Message- >From: "Berk Hess" <[EMAIL PROTECTED]> >To: gmx-users@gromacs.org >Date: Fri, 23 Nov 2007 10:36:57 +0100 >Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD > > > > > >From: "OZGE ENGIN" <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > >To: gmx-users@gromacs.org > >Subject: [gmx-users] problem with mdrun performing replica exchange MD > >Date: Fri, 23 Nov 2007 11:30:53 +0200 > > > >Hi All, > > > >I am performing replica exchange molecular dynamics simulation(REMD). I > >have 16 replicas each of which has a peptide with different conformation. > >After obtaining .tpr files (at desired temperatures) for each replicas, I > >loaded them via mdrun, but I got the following error: > > > >Fatal error: > >Nothing to exchange with only one replica > >--- > > > >Why? > >I guess there are two possibilities. >Or you did not use the -np option of mdrun to set the number of replicas, >or you have not compiled Gromacs with MPI support. > >Berk. > >_ >Talk with your online friends with Messenger >http://www.join.msn.com/messenger/overview > >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problem with mdrun performing replica exchange MD
OZGE ENGIN wrote: This time, I used the following command line: mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8 rename rename your tpr files to simul_md0.tpr simul_md1.tpr ... simul_md7.tpr but I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul00.tpr --- "Shit Happens" (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 Although I do not have such a file: simul00.tpr -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:44:47 +0200 Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:30:53 +0200 Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: Nothing to exchange with only one replica --- Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please d
Re: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
This time, I used the following command line: mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8 but I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul00.tpr --- "Shit Happens" (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 Although I do not have such a file: simul00.tpr -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange >MD >Date: Fri, 23 Nov 2007 11:44:47 +0200 > >Hi Berk, > >I indicated the number of replicas with -multi option. In additon, I have >compiled Gromacs with MPI support. > >I used the following command line: > >mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 > >-Original Message- >From: "Berk Hess" <[EMAIL PROTECTED]> >To: gmx-users@gromacs.org >Date: Fri, 23 Nov 2007 10:36:57 +0100 >Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD > > > > > >From: "OZGE ENGIN" <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > >To: gmx-users@gromacs.org > >Subject: [gmx-users] problem with mdrun performing replica exchange MD > >Date: Fri, 23 Nov 2007 11:30:53 +0200 > > > >Hi All, > > > >I am performing replica exchange molecular dynamics simulation(REMD). I > >have 16 replicas each of which has a peptide with different conformation. > >After obtaining .tpr files (at desired temperatures) for each replicas, I > >loaded them via mdrun, but I got the following error: > > > >Fatal error: > >Nothing to exchange with only one replica > >--- > > > >Why? > >I guess there are two possibilities. >Or you did not use the -np option of mdrun to set the number of replicas, >or you have not compiled Gromacs with MPI support. > >Berk. > >_ >Talk with your online friends with Messenger >http://www.join.msn.com/messenger/overview > >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:44:47 +0200 Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] problem with mdrun performing replica exchange MD >Date: Fri, 23 Nov 2007 11:30:53 +0200 > >Hi All, > >I am performing replica exchange molecular dynamics simulation(REMD). I >have 16 replicas each of which has a peptide with different conformation. >After obtaining .tpr files (at desired temperatures) for each replicas, I >loaded them via mdrun, but I got the following error: > >Fatal error: >Nothing to exchange with only one replica >--- > >Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: "Berk Hess" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] problem with mdrun performing replica exchange MD >Date: Fri, 23 Nov 2007 11:30:53 +0200 > >Hi All, > >I am performing replica exchange molecular dynamics simulation(REMD). I >have 16 replicas each of which has a peptide with different conformation. >After obtaining .tpr files (at desired temperatures) for each replicas, I >loaded them via mdrun, but I got the following error: > >Fatal error: >Nothing to exchange with only one replica >--- > >Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] problem with mdrun performing replica exchange MD
From: "OZGE ENGIN" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:30:53 +0200 Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: Nothing to exchange with only one replica --- Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
