Hi justin, Thanks for the suggestion. I will look at the code. Meanwhile I have one doubt regarding the following option of the g_msd tool.
“-trestart time 10 Time between restarting points in trajectory (ps)” What does this -trestart indicates actually. I did a small trail run on a 100ps trajectory (containing 500 snapshots) with snapshots collected at .2ps interval. In the output file, it is printed as “# MSD gathered over 100 ps with 11 restarts”. Does it mean that the MSD is calculated with 11 different reference coordinates. Thanks, Bala On Tue, Aug 21, 2012 at 4:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/21/12 10:01 AM, Bala subramanian wrote: >> >> Friends, >> I have calculate the mean sq. displacement of water molecules in the first >> hydration shell around the protein (distance of .25nm). I want to write >> the >> code but i dnt know how to manipulate the coordinates to account for the >> pbc. Any guidance from anyone would be a great help. > > > Why not just run g_msd with an index file? The closest water molecules can > be reordered using trjorder. Dynamic selections can be made with g_select, > though those index groups cannot be used directly, but you can get something > very close with trjorder + make_ndx. > > Otherwise, see the existing code in g_msd for how it works. It sounds like > you'll be reusing most of its code anyway. > > -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 list gmx-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 -- C. Balasubramanian -- gmx-users mailing list gmx-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