[gmx-users] g_msd and Diffusion coefficient
YossiT at tauex.tau.ac.il
Thu Apr 26 10:36:25 CEST 2007
1. I have an .xtc and .tpr files of a simulation (protein, ligand,
ions and spc216 water) which were performed on gromacs 3.2.1 two years
ago. When I run g_msd based on these files on a specific water molecule
in gromacs 3.3.1 and on gromacs 3.2.1, I get different charts (msd vs.
t) and different values for the diffusion coefficient. What do you
recommend to "trust", the new version results or should I perform all
analysis procedure on these files on gromacs 3.2.1?
2. When I run g_msd on a specific water residue with and without
the option -mol I get different values for D and again different charts
of msd vs. time. Can you clarify more about the option -mol?
Thank you all,
Dr. Yossi Tsfadia
Tel Aviv University
Faculty of Life Sciences
E-mail: yossit at tauex.tau.ac.il
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