[gmx-users] Umbrella Sampling Force component output
Dear Gromacs Users, I runned and Umbrella Sampling simulation but I made a mistake in the value of the pull_dim option, so gromacs printed the z component of the force instead of the x component that i need (with the option -pf of mdrun). I have all files from the simulation. Is there a way to get the x component of the force without running the simulation again? Thanks in advanced, Kenny -- 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] Umbrella Sampling Force component output
Thanks Erik On 06/12/2013 01:50 PM, Erik Marklund wrote: Hi, No, I'm afraid not. pull-dim not only determines what components are to be printed, it also determines in what dimensions the force is to be applied during the simulation. Erik On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez ke...@mpi-muelheim.mpg.de wrote: Dear Gromacs Users, I runned and Umbrella Sampling simulation but I made a mistake in the value of the pull_dim option, so gromacs printed the z component of the force instead of the x component that i need (with the option -pf of mdrun). I have all files from the simulation. Is there a way to get the x component of the force without running the simulation again? Thanks in advanced, Kenny -- 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 -- 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 -- 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] REMD simulation
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 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 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? Readhttp://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? Readhttp://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 -- 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] Extending REMD simulations problem
Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-1 Global communication frequency -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]cpnum bool no Keep and number checkpoint files -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names -maxhreal -1 Terminate after 0.99 times this time (hours) -multi int2 Do multiple simulations in parallel -replex int500 Attempt replica exchange every # steps -reseed int-1 Seed for replica exchange, -1 is generate a seed -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system node 0 par_fn 'testl_1.tpr' node 0 par_fn 'test_1.trr' node 0 par_fn 'test_1.xtc' node 0 par_fn 'test_1.cpt' node 0 par_fn 'test_1.cpt' node 0 par_fn 'test_1.gro' node 0 par_fn 'test_1.edr' node 0 par_fn 'test_1.log' log node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.xtc' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.edo' node 0 par_fn 'test_1.gct' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_0.log' log node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xtc' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.edo' node 0 par_fn 'test_0.gct' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.xvg' node 0 par_fn 'test_0.mtx' node 0 par_fn 'test_0.ndx' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.xvg' node 0 par_fn 'test_1.mtx' node 0 par_fn 'test_1.ndx' Multi-checking simulation part ... OK Multi-checking simulation part ... OK Reading file testl_0.tpr, VERSION 4.5.5 (double precision) Reading file testl_1.tpr, VERSION 4.5.5 (double precision) Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... ERROR: 0031-250 task 4: Segmentation fault ERROR: 0031-250 task 5: Segmentation fault ERROR: 0031-250 task 0: Terminated ERROR: 0031-250 task 3: Terminated ERROR: 0031-250 task 1: Segmentation fault ERROR: 0031-250 task 2: Segmentation fault -- 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 -- 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] REMD simulation
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 server 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 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
