Re: [gmx-users] REMD As A Function of Distance Between 2 Chains
plz stop mailing me. - Original Message From: Huey Ling Tan [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 14 November, 2007 11:23:01 PM Subject: Re: [gmx-users] REMD As A Function of Distance Between 2 Chains Dear all , thank you for those comments, we are aware of the paper. However, we are not sure how to implement the replica exchange in gromacs. We would like to run a set of replicas in which each replica corresponds to a different set of umbrella parameters. However, when setting up a replica exchange run, all .tpr files use the same .ppa file so that each replica will have the same umbrella potential parameters. Do you know how to get around this problem. Thank you in advance, Huey Ling On 13/11/2007, Marcus Kubitzki [EMAIL PROTECTED] wrote: Hi Huey Ling, have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for details on Hamiltonian REMD, especially the correct exchange criterion. In their paper, they discuss in detail what you want to do, namely Replica Exchange Umbrella Sampling. Marcus Huey Ling Tan wrote: Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? If anyone know how this can be done? Many thanks. -- Best regards, Huey Ling ___ 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 -- Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ ___ 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 -- Best regards, Huey Ling -Inline Attachment Follows- ___ 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 ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html___ 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 As A Function of Distance Between 2 Chains
Huey Ling Tan wrote: Dear all , thank you for those comments, we are aware of the paper. However, we are not sure how to implement the replica exchange in gromacs. We would like to run a set of replicas in which each replica corresponds to a different set of umbrella parameters. However, when setting up a replica exchange run, all .tpr files use the same .ppa file so that each replica will have the same umbrella potential parameters. Do you know how to get around this problem. You will have to change the code to implement this algorithm. 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 As A Function of Distance Between 2 Chains
Mark Abraham wrote: Huey Ling Tan wrote: Dear all , thank you for those comments, we are aware of the paper. However, we are not sure how to implement the replica exchange in gromacs. We would like to run a set of replicas in which each replica corresponds to a different set of umbrella parameters. However, when setting up a replica exchange run, all .tpr files use the same .ppa file so that each replica will have the same umbrella potential parameters. Do you know how to get around this problem. You will have to change the code to implement this algorithm.' But first check the pull code in the cvs version of gromacs, where all options have been moved to the mdp file. 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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
Re: [gmx-users] REMD As A Function of Distance Between 2 Chains
Hi Huey Ling, have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for details on Hamiltonian REMD, especially the correct exchange criterion. In their paper, they discuss in detail what you want to do, namely Replica Exchange Umbrella Sampling. Marcus Huey Ling Tan wrote: Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? If anyone know how this can be done? Many thanks. -- Best regards, Huey Ling ___ 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 -- Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ ___ 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 As A Function of Distance Between 2 Chains
Dear Huey Ling, In principle it is applicable. Then such REMD can be termed as Hamiltonian REMD instead of canonical temperature REMD. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huey Ling Tan Sent: Tuesday, November 13, 2007 2:24 AM To: Discussion list for GROMACS users Subject: [gmx-users] REMD As A Function of Distance Between 2 Chains Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? If anyone know how this can be done? Many thanks. -- Best regards, Huey Ling ___ 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
