Hi, if you want to calculate the MSD of several molecules, say nrmol, without using the -mol option, which I do not know is still broken, you can do this in three simple steps:
1. Convert your trajectory with trjconv and the option -pbc whole
2. Create an index file, that contains groups, which contain one
molecule each, and remove the standard groups like System ...
3. run the analysis with: echo {0..nrmol} | g_msd -f convertedtrajecotry
-n indexfile -ng nrmol
This gives you the correct MSD for the center of mass for every
molecule.
Cheers,
Flo
* George Patargias <g...@bioacademy.gr> [2013-05-02 10:08:20 +0300]:
Thanks for this Vitaly and Justin. GeorgeThe resulting MSD will correspond to the average from individual atoms. Calculating MSD of an individual atom and ascribing it to a [small] molecule, which this atom belongs to, is reasonable. Assuming that averaged MSD from atoms correspond to the cluster they form is not. Dr. Vitaly Chaban On Wed, May 1, 2013 at 2:40 PM, George Patargias <g...@bioacademy.gr> wrote:Hello I am trying to calculate the MSD of 8 molecules in a lipid bilayer with g_msd. If I include the atoms of all these 8 molecules as a single group in the index file, will g_msd calculate the MSD of the center of mass of them or it will average over all atoms? Thanks George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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 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_ListsDr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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
-- Dr.rer.nat. Florian Dommert Institute for Computational Physics University Stuttgart Allmandring 3 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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