Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong for calculating the msd.
On Tuesday, October 7, 2014, pratibha kapoor <kapoorpratib...@gmail.com> wrote: > Hi all > > I have created my own code for msd calculation and would like to verify it > from g_msd. I have created pdb files using trjconv -center -pbc whole > option. Can I use the coordinates in pdb as such (with no > wrapping/unwrapping/shifting) for running my code? or does the inbuild > g_msd program modifies them (shift)? > My msd values are not matching with the g_msd values. I suspect that > discrepency in the pdb file creation since the values obtained from my > program agrees with manual calculation (of some dummy values). > Any suggestions are highly welcomed. > -- > 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 <javascript:;>. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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.