[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
Re: [gmx-users] REMD simulation
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.phphttp://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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists --
Re: [gmx-users] REMD simulation
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 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 -- 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
Re: [gmx-users] REMD simulation
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 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 -- 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
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 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
[gmx-users] REMD simulation of peptide-membrane system
Dear all, I'd like to do folding simulations of a short peptide on membrane surface using REMD using atomistic FF. But the problem is that membrane will disrupt at high temperatures. To maintain the membrane structure, I am thinking the following two methods: (1) To use different coupling temperature for different groups (e.g., keeping membrane at 323K for all the replicas, but keeping peptide and water with different temperatures). Will this lead to artifact? (2) If this leads to serious artifact, I may need to use constraints on the membrane, as mentioned in the paper from Berkowitz group. Is there any other method for the above problem? Any comments is greatly appreciated, thank you in advance, Cheers, Jianguo -- 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] REMD simulation of peptide-membrane system
On 03/03/11, Jianguo Li ljg...@yahoo.com.sg wrote:
!-- DIV {margin:0px;} --
Dear all,
I'd like to do folding simulations of a short peptide on membrane surface
using REMD using atomistic FF. But the problem is that membrane will disrupt
at high temperatures. To maintain the membrane structure, I am thinking the
following two methods:
(1) To use different coupling temperature for different groups (e.g., keeping
membrane at 323K for all the replicas, but keeping peptide and water with
different temperatures). Will this lead to artifact?
Yes. You will have heat flowing via the system between two external heat baths.
(2) If this leads to serious artifact, I may need to use constraints on the
membrane, as mentioned in the paper from Berkowitz group.
That seems more wise, but still not great.
Mark
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