Re: [gmx-users] REMD problem
Liu, Liang wrote: Thanks. Actually I applied just because the tutorial said so :( What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :( What structure(s)? The .xtc files contain the coordinates along each trajectory (ensemble-continuous), and the final snapshot is written to a .gro file by mdrun (although these do not necessarily tell you anything by themselves). I am totally fresh to MD simulation, just worked on this for 1 week ... Back up. REMD can be very complex, especially if you want to do it right. Do some basic tutorial material (standard MD) and understand the workflow and analysis. Spend time in the literature, as Mark suggested. The time investment you make now may delay your actual data collection by a few weeks, but will save you months of wasted time overall if you try to plow ahead without a clear vision for what you're doing. -Justin On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 30/09/2011 2:50 AM, Liu, Liang wrote: After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Yep. One for each simulation. Not sure if the result is reasonable. Justin told you yesterday they would not be, because you have made a number of totally arbitrary choices. I tried to analyze the result, and after applying demux.pl http://demux.pl/, two files replica_index.xvg replica_temp.xvg are obtained. Why did you want to demux? My question is how to obtain the structure information? (I will need pdb file). Do all the tutorial material you can find - even if not strictly relevant - to get an idea about good workflows. Then try to replicate (part of) a published REMD study to see how things work there. Search the web and check out the GROMACS web page - there's lots of material out there. Stabbing in the dark is a great way to waste your time, and people here don't have the time to teach every person every thing. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 problem
After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My question is how to obtain the structure information? (I will need pdb file). On Thu, Sep 29, 2011 at 6:23 AM, Manuel Prinz man...@pinguinkiste.dewrote: Am Do, 29.09.2011, 01:38 schrieb Mark Abraham: If the MPI configuration allows physical processors to be over-allocated, then GROMACS is none the wiser. Over-allocation is the default in Open MPI[1]. So it's technically possible to run 50 MPI processes on 2 cores. Whether or not this is a good idea is left on as an exercise to the reader. ;) Best regards, Manuel [1] When not run from a resource manager that takes care of setting the right configuration options. -- 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 -- Best, Liang Liu -- 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 problem
After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My question is how to obtain the structure information? (I will need pdb file). -- 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 problem
On 30/09/2011 2:50 AM, Liu, Liang wrote: After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Yep. One for each simulation. Not sure if the result is reasonable. Justin told you yesterday they would not be, because you have made a number of totally arbitrary choices. I tried to analyze the result, and after applying demux.pl http://demux.pl/, two files replica_index.xvg replica_temp.xvg are obtained. Why did you want to demux? My question is how to obtain the structure information? (I will need pdb file). Do all the tutorial material you can find - even if not strictly relevant - to get an idea about good workflows. Then try to replicate (part of) a published REMD study to see how things work there. Search the web and check out the GROMACS web page - there's lots of material out there. Stabbing in the dark is a great way to waste your time, and people here don't have the time to teach every person every thing. Mark -- 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 problem
Thanks. Actually I applied just because the tutorial said so :( What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :( I am totally fresh to MD simulation, just worked on this for 1 week ... On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 30/09/2011 2:50 AM, Liu, Liang wrote: After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Yep. One for each simulation. Not sure if the result is reasonable. Justin told you yesterday they would not be, because you have made a number of totally arbitrary choices. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. Why did you want to demux? My question is how to obtain the structure information? (I will need pdb file). Do all the tutorial material you can find - even if not strictly relevant - to get an idea about good workflows. Then try to replicate (part of) a published REMD study to see how things work there. Search the web and check out the GROMACS web page - there's lots of material out there. Stabbing in the dark is a great way to waste your time, and people here don't have the time to teach every person every thing. Mark -- 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 -- Best, Liang Liu -- 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 problem
Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. -- Best, Liang Liu -- 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 problem
Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 problem
Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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 problem
Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 problem
Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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 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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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 problem
Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users 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 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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto: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
Re: [gmx-users] REMD problem
This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/** Documentation/How-tos/REMD#___**_Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__** Documentation/How-tos/REMD#__**Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#** Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org** http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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 http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search 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
Re: [gmx-users] REMD problem
Liu, Liang wrote: This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Current Gromacs versions allow more than one processor per REMD simulation. Please refer to the link I provided before for specifics. You need all of the replicas to run at roughly the same speed so the number of processors per simulation should be the same. Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? It's just like any other simulation in this regard. -Justin Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/__justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] REMD problem
So if my personal computer have 2 cores, the np should be set to 2? Does it relate to -multi? How to choose a reasonable number for -replex? the smaller the better? Thanks again. On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Current Gromacs versions allow more than one processor per REMD simulation. Please refer to the link I provided before for specifics. You need all of the replicas to run at roughly the same speed so the number of processors per simulation should be the same. Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? It's just like any other simulation in this regard. -Justin Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__** Documentation/How-tos/REMD#___**___Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#___** _Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/** Documentation/How-tos/REMD#___**_Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/** Documentation/How-tos/REMD#___**_Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__** Documentation/How-tos/REMD#__**Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#** Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA
Re: [gmx-users] REMD problem
Liu, Liang wrote: So if my personal computer have 2 cores, the np should be set to 2? Does it relate to -multi? That means you can only run 2 replicates. Bad idea. You'll need access to a much better cluster to do anything meaningful. All REMD simulations have to be run simultaneously. If you want 50 replicas, you need at least 50 processors, ideally more. How to choose a reasonable number for -replex? the smaller the better? Please consult the literature. -Justin Thanks again. On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Current Gromacs versions allow more than one processor per REMD simulation. Please refer to the link I provided before for specifics. You need all of the replicas to run at roughly the same speed so the number of processors per simulation should be the same. Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? It's just like any other simulation in this regard. -Justin Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps
Re: [gmx-users] REMD problem
Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. Thanks. -- Best, Liang Liu -- 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 problem
Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 problem
Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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 problem
Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 problem
Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+040.0e+00 PotentialKinetic En. Total Energy Conserved En.Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+105.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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 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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of
Re: [gmx-users] REMD problem
Liu, Liang wrote: Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+040.0e+00 PotentialKinetic En. Total Energy Conserved En.Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+105.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling. -Justin On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] REMD problem
On 29/09/2011 7:20 AM, Justin A. Lemkul wrote: Liu, Liang wrote: Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.0e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+10 5.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling. If the MPI configuration allows physical processors to be over-allocated, then GROMACS is none the wiser. Mark -Justin On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users
Re: [gmx-users] REMD problem
Not know. I will update the result tomorrow, as the 5 steps take really long time :( On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/09/2011 7:20 AM, Justin A. Lemkul wrote: Liu, Liang wrote: Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.0e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+10 5.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling. If the MPI configuration allows physical processors to be over-allocated, then GROMACS is none the wiser. Mark -Justin On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] REMD problem in concept
dG=dH-TdS so as T increases, so does the entropic contribution to the free energy (=available energy). The potential energies stay the same when using a temperature-independent forcefield (like all of the ones that come with gromacs). Your system will easily cross barriers on the order of KbT and thus barriers are more easily crossed at higher temperature. Nearly every RE paper has an introductory section that goes over these topics in more or less detail. I suggest that you read the introduction and theory sections of about 10 of them and you should by then understand it very well. Chris. -- original message -- Hi, Thank you for the reply. But in that case what helps the replica at higher temperature cross the energy barrier? At higher temperature the velocities will be higher. Thanks in advance, Sarbani On Tue, 02 Dec 2008 Mark Abraham wrote : [Hide Quoted Text] sarbani chattopadhyay wrote: Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. Kinetic energy is a function of the velocities, potential energy is a function of the positions. So velocity rescaling will not have any instantaneous effect on the PE. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? As before, nothing. I may be missing a very basic point and any suggestion regarding this will be highly helpful. Once the simulation continues, things are still normal. The reason the exchange occurred was that the positions were such that the PE was close enough that detailed balance for the generalized ensemble was preserved during the swap. Thus the ensembles before and after the exchange are also still well-formed. Mark ___ 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] REMD problem in concept
[EMAIL PROTECTED] wrote: dG=dH-TdS so as T increases, so does the entropic contribution to the free energy (=available energy). The potential energies stay the same when using a temperature-independent forcefield (like all of the ones that come with gromacs). That's not quite right. The average total energy (H, above) increases with T, and the equipartition theorem requires that for a typical MD system in thermal equilibrium, some of that energy must go to increased average PE. The form of the forcefield doesn't change, of course. This KE-PE-TE behaviour can be readily observed in an REMD simulation and is documented in various graphs in various REMD papers. Your system will easily cross barriers on the order of KbT and thus barriers are more easily crossed at higher temperature. Nearly every RE paper has an introductory section that goes over these topics in more or less detail. I suggest that you read the introduction and theory sections of about 10 of them and you should by then understand it very well. Yep, agreed. Mark ___ 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] REMD problem in concept
Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? I may be missing a very basic point and any suggestion regarding this will be highly helpful. Thanking you, Sarbani ___ 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] REMD problem in concept
sarbani chattopadhyay wrote: Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. Kinetic energy is a function of the velocities, potential energy is a function of the positions. So velocity rescaling will not have any instantaneous effect on the PE. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? As before, nothing. I may be missing a very basic point and any suggestion regarding this will be highly helpful. Once the simulation continues, things are still normal. The reason the exchange occurred was that the positions were such that the PE was close enough that detailed balance for the generalized ensemble was preserved during the swap. Thus the ensembles before and after the exchange are also still well-formed. Mark ___ 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] REMD problem in concept
Hi, Thank you for the reply. But in that case what helps the replica at higher temperature cross the energy barrier? At higher temperature the velocities will be higher. Thanks in advance, Sarbani On Tue, 02 Dec 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. Kinetic energy is a function of the velocities, potential energy is a function of the positions. So velocity rescaling will not have any instantaneous effect on the PE. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? As before, nothing. I may be missing a very basic point and any suggestion regarding this will be highly helpful. Once the simulation continues, things are still normal. The reason the exchange occurred was that the positions were such that the PE was close enough that detailed balance for the generalized ensemble was preserved during the swap. Thus the ensembles before and after the exchange are also still well-formed. Mark ___ 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
