Dear All, I am using 'gmx_mpi sasa' module as below:
gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q surface.pdb -surface -b 50000 Now, surface.pdb file will generate the surface of the selected portion together with the coordinates of all the atoms present in the protein. Are the coordinates of all atoms of the protein averaged over the selected range of trajectory or they are averaged over the range of trajectory supplied in the .xtc file (as for example, here, I have selected 50-100 ns, though my .xtc file ranges from 0-100 ns)? Thanks in advanced! Best wishes, Sudip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
