That looks very strange. Please file an issue at redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to me.
Mark On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez < ke...@mpi-muelheim.mpg.de> wrote: > Hi all, > > and thanks Mark, Chris and Xavier for your comments. > > I finally managed to run the REMD simulation but i can not restart the > simulation or continue the simulation after it finished. > I tried with a test system and run two replicas for just 20 ps. After it > finished correctly i extended the time in each .tpr file > and tried to continue the REMD simulation using the checkpoint files but i > always get the same error message > > Multi-checking simulation part ... OK > Multi-checking simulation part ... OK > Reading file test0.tpr, VERSION 4.5.5 (single precision) > Reading file test1.tpr, VERSION 4.5.5 (single precision) > Multi-checking simulation part ... Multi-checking simulation part ... > Multi-checking simulation part ... Multi-checking simulation part ... > Multi-checking simulation part ... Multi-checking simulation part ... > ERROR: 0031-250 task 6: Segmentation fault > ERROR: 0031-250 task 7: Segmentation fault > ERROR: 0031-250 task 2: Segmentation fault > ERROR: 0031-250 task 1: Segmentation fault > ERROR: 0031-250 task 5: Segmentation fault > ERROR: 0031-250 task 3: Segmentation fault > ERROR: 0031-250 task 0: Terminated > ERROR: 0031-250 task 4: Terminated > > I used Gromacs 4.5.5 and the following commands: > > to start the REMD simulation: > mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 > > to extend the time of the simulation in the .tpr files: > tpbconv_d -s test_#.tpr -extend 20 -o test_#.tpr > > to continue the REMD simualtion: > mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 > > Do i need to use any specific option to be able to continue the REMD > simulation? > > Thanks in advanced > Kenny > > > > > > > Virtual sites also have a hidden benefit - not only can you take a longer >> time step, but the width of the distribution of PE is relatively wider, >> so >> you can have higher exchange probability for the same temperatures. >> >> Mark >> >> On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale< >> chris.ne...@mail.utoronto.ca> wrote: >> >> > Xavier is right, except that you can also reduce the size of your >> system. >> > You can take larger steps in temperature >> > if you have fewer atoms. If you are using a cubic system, you can >> move to >> > a rhombic dodecahedron. >> > Even constraining all bonds will help a bit here (vs. harmonic bonds). >> > There are lots of papers on this topic. >> > >> > To see why you don't get any exchanges, construct histograms of your >> > potential energies and you will see >> > that they don't overlap. Also, it is inefficient to take evenly spaced >> > temperatures. This is not your major problem, >> > but read a bit on exponentially spaced temperatures for REMD. >> > >> > Chris. >> > >> > -- original message -- >> > >> > Well either you use more replicas or you reduce the temperature >> > range ... >> > There is no way around! >> > >> > On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: >> > >> > > Dear All, >> > > >> > > i am trying to performed REMD simulations using Gromacs. >> > > My question is concerning the temperature distribution and the >> > > number of replica. >> > > I need to run 24 replicas of my system with a temperature range of >> > > 290-400 K. How can I select the temperatures values for each >> replica? >> > > I tried the >> serverhttp://folding.bmc.uu.**se/remd/index.php<http://folding.bmc.uu.se/remd/index.php> >> but for >> > > my system it gives 50 replicas. If i try to take 24 evenly spaced >> > > values from the obtained list of temperature then >> > > the replicas do not exchange at all. >> > > I am using Gromacs 4.5.5 and my system has 6862 water molecules and >> > > 535 atoms for the solute. >> > > >> > > Thanks in advanced >> > > Kenny >> > > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > * Please search the archive at >> > >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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? >> Readhttp://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at > http://www.gromacs.org/**Support/Mailing_Lists/Search<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? > Readhttp://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > > -- > Kenny Bravo Rodriguez > Max-Planck-Institut für Kohlenforschung > Kaiser-Wilhelm-Platz 1 > D-45470 Mülheim an der Ruhr > Germany > Phone: +49 (0)208 306 2160 > Email:ke...@mpi-muelheim.mpg.**de <email%3ake...@mpi-muelheim.mpg.de> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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