RE: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation
Those tutorials show most important things (e.g. how to build topology for given system) in CG Martini ff using Gromacs. You do not have to merge anything. Commands are the same as for atomistic simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of J Peterson [think_bey...@aol.com] Sent: Tuesday, August 07, 2012 5:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the available Martini files and programs with the recent version of GROMACS that is version 4? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p486.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] RE: tutorials for Coarse-Grained MD Simulation
Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How do I do this step.? These files are also tested with Gormacs 3.3.1 version, how do they work with recent versions of GROMACS? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p492.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] RE: tutorials for Coarse-Grained MD Simulation
On 8/7/12 6:51 AM, J Peterson wrote: Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How do I do this step.? Follow whatever instructions they provide for the installation. It's probably just a modified version of Gromacs with an additional tool, so the installation would be like any you would do for a normal Gromacs distribution. Make sure to set a proper installation path to avoid overwriting your existing Gromacs installation. These files are also tested with Gormacs 3.3.1 version, how do they work with recent versions of GROMACS? They don't. People have discussed this problem previously. In theory, you could probably re-create whatever necessary input files (.top, .tpr, etc) under version 3.3.1 and process any trajectories created with more modern versions. Version 3.3.1 is ancient and there have been hundreds of bug fixes and feature enhancements since it came out. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] RE: tutorials for Coarse-Grained MD Simulation
Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the available Martini files and programs with the recent version of GROMACS that is version 4? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p486.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
