[gmx-users] converting Desmond trajectories to Gromacs
Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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] converting Desmond trajectories to Gromacs
On 26/07/2012 5:01 PM, Nidhi Jatana wrote: Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? http://www.gromacs.org/Documentation/How-tos/Using_VMD_plugins_to_read_trajectory_formats_not_native_to_GROMACS Mark -- 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] converting Desmond trajectories to Gromacs
Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- 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] converting Desmond trajectories to Gromacs
On 7/24/12 6:13 AM, Nidhi Jatana wrote: Dear Sir/Madam I am running simulations on a membrane protein using Desmond and I want to calculate area per lipid for the entire trajectory. I can convert the trajectories to those of Gromacs using VMD. What else do I need in order to calculate area per lipid using Gromacs? The area per lipid is not a trivial quantity to calculate when there's a protein involved, and there is no Gromacs tool that will do it. We created a program a few years ago that does, but note that you cannot analyze a trajectory, only a single coordinate file (.gro or .pdb). The current workaround is to dump out a series of coordinate files and loop over all of them in a shell script. Note that, depending on how many frames you have in your trajectory, this may take quite a while - APL calculations typically take on the order of 2-5 minutes (per frame), depending on how large the system is. http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ -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
