[gmx-users] Hamiltonian replica exchange not working in 4.6
Dear Gromacs user, I am not sure whether this is any potential bug. But I found that in gromacs4.6.3, hamiltonian replica exchange simulation is not working. The SAME simulation works perfectly fine in gromacs 4.5.4 But, when I try to run the simulation using gromacs4.6.3, I get following error: The properties of the 10 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS Here is the details on the error: I have first defined A and B state by scaling the relevant parameter.. Then I have generated different tpr file by using mdp file which only differ by 'init-lambda' parameter: For example, I have 10 different mdp files: Free energy part of two of them are shown below: for hremd0.mdp, the relevant part for free energy part is ; Free energy control stuff free_energy = yes init-lambda = 0 delta_lambda = 0 for hremd1.mdp ; Free energy control stuff free_energy = yes init-lambda = .080 delta_lambda = 0 .. and so on.. The rest of mdp portions are same for all the mdp files... However, with gromacs4.5.4, the same simulation works without problem. I do not get the error that all the systems are identical. In both cases, I am using same system with OPLS forcefield.. The way I run the simulations is: mpirun -np 10 mdrun_463 -multi 10 -v -s hremd -replex 250 -c log_repl Any help will be appreciated. Sanku -- 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] Hamiltonian replica exchange not working in 4.6
Hi, Sanku- The way to invoke Hamiltonian replica exchange has changed to be a bit more flexible. We should go back and make sure that this legacy way is supported (I thought this invocation was supported, but apparently it isn't), but what you should be able to do to get it working quickly is include in all the .mdp files the line: fep-lambdas 0 0.08 . . . . . . 1.0 I.e. list all of the lambdas that all of the files use. This is described in the documentation. It should run correctly then. If not, then bug me on the list again. On Tue, Aug 6, 2013 at 6:52 PM, Sanku M msank...@yahoo.com wrote: Dear Gromacs user, I am not sure whether this is any potential bug. But I found that in gromacs4.6.3, hamiltonian replica exchange simulation is not working. The SAME simulation works perfectly fine in gromacs 4.5.4 But, when I try to run the simulation using gromacs4.6.3, I get following error: The properties of the 10 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS Here is the details on the error: I have first defined A and B state by scaling the relevant parameter.. Then I have generated different tpr file by using mdp file which only differ by 'init-lambda' parameter: For example, I have 10 different mdp files: Free energy part of two of them are shown below: for hremd0.mdp, the relevant part for free energy part is ; Free energy control stuff free_energy = yes init-lambda = 0 delta_lambda = 0 for hremd1.mdp ; Free energy control stuff free_energy = yes init-lambda = .080 delta_lambda = 0 .. and so on.. The rest of mdp portions are same for all the mdp files... However, with gromacs4.5.4, the same simulation works without problem. I do not get the error that all the systems are identical. In both cases, I am using same system with OPLS forcefield.. The way I run the simulations is: mpirun -np 10 mdrun_463 -multi 10 -v -s hremd -replex 250 -c log_repl Any help will be appreciated. Sanku -- 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] Hamiltonian replica exchange umbrella sampling with gmx 4.6
Dear gmx-users, I am currently trying to runt Hamiltonian replica exchange umbrella sampling in hope to do some better sampling. I have generated a number of tpr-files along my reaction coordinate and they all run fine in independent simulations. The issue comes when I would like the replica exchange to start. The following line is used to initiate the exchange: mdrun_mpi -replex 1000 -s md -pf pullf -px pullx -multi 40 -maxh 0.5 All replicas have the same temperature and the following error is what I face seconds after submitting the job: The properties of the 40 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I could simply change the temperature between the replicas by 0.001 K and it would run I think. But that is not very elegant. Does anyone have any suggestions? Thanks in advance! Best regards, Joakim-- 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] Hamiltonian replica exchange umbrella sampling with gmx 4.6
Hi, Joakim- Hamiltonian exchange only should work if there is a lambda coupling parameter that defines the potential at each state. You need to define your pulling potential so that the coupling-lambda parameter can be used to define the different pulling location centers along your trajectory. Does this make it clearer? On Thu, Mar 7, 2013 at 7:26 AM, Joakim Jämbeck jamb...@me.com wrote: Dear gmx-users, I am currently trying to runt Hamiltonian replica exchange umbrella sampling in hope to do some better sampling. I have generated a number of tpr-files along my reaction coordinate and they all run fine in independent simulations. The issue comes when I would like the replica exchange to start. The following line is used to initiate the exchange: mdrun_mpi -replex 1000 -s md -pf pullf -px pullx -multi 40 -maxh 0.5 All replicas have the same temperature and the following error is what I face seconds after submitting the job: The properties of the 40 systems are all the same, there is nothing to exchange For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I could simply change the temperature between the replicas by 0.001 K and it would run I think. But that is not very elegant. Does anyone have any suggestions? Thanks in advance! Best regards, Joakim-- 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] Hamiltonian replica exchange?
Hi, I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? Sanku-- 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] Hamiltonian replica exchange?
Hamiltonian replica exchange is planned for 4.6, and is being beta tested by some users. On Tue, Aug 16, 2011 at 2:39 PM, Sanku M msank...@yahoo.com wrote: Hi, I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? Sanku -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Hamiltonian replica exchange ?
Hi, I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? Sanku-- 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] Hamiltonian replica exchange
Hi, What do you mean exactly with Hamiltonian replica exchange? There is a (hidden) implementation of Hamiltonian exchange for the free energy coupling parameter lambda in 4.0. This uses delta_lambda*dH/dlambda iso delta_H, which is why it is hidden. In 4.1 we will use delta_H. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Tue, 14 Oct 2008 14:20:55 -0300 Subject: [gmx-users] Hamiltonian replica exchange Hi, Is Hamiltonian replica exchange implemented in gmx 4.0? can't find it in the manual. Marcos. ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] Hamiltonian replica exchange
On Wed, 2008-10-15 at 10:43 +0200, Berk Hess wrote: Hi, What do you mean exactly with Hamiltonian replica exchange? I would like to do H-RexMD with backbone torsional bias, as an alternative to T-RexMD for peptide folding. Each replica run at the same Temp but with a different force field. The replicas are exchanged according to Delta = beta [ En(Xm) - Em(Xm) + Em(Xn) - En(Xn) ] if the energy on every replica differs only by a torsional potential bias V(X) scaled by f(i) in every replica i, En(Xm) - Em(Xm) = [f(n) - f(m)] V(Xm) and Delta = beta [f(n) - f(m)] [V(Xm) - V(Xn)] This is eq. 8 in Affentranger et. al. http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2006/2/i02/abs/ct050250b.html The idea of backbone torsional bias is from Kannan and Zacharias http://www.ncbi.nlm.nih.gov/pubmed/17120231 They fold peptides with only 5-7 replicas. Saludos, Marcos. There is a (hidden) implementation of Hamiltonian exchange for the free energy coupling parameter lambda in 4.0. This uses delta_lambda*dH/dlambda iso delta_H, which is why it is hidden. In 4.1 we will use delta_H. Berk __ From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Tue, 14 Oct 2008 14:20:55 -0300 Subject: [gmx-users] Hamiltonian replica exchange Hi, Is Hamiltonian replica exchange implemented in gmx 4.0? can't find it in the manual. Marcos. ___ gmx-users mailing list gmx-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 __ Express yourself instantly with MSN Messenger! MSN Messenger ___ 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
[gmx-users] Hamiltonian replica exchange
Hi, Is Hamiltonian replica exchange implemented in gmx 4.0? can't find it in the manual. Marcos. ___ 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] Hamiltonian replica exchange
marcos wrote: Hi, Is Hamiltonian replica exchange implemented in gmx 4.0? can't find it in the manual. No. 4.1 Marcos. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please 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
