Dear all,
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, Yossi Tsfadia Dr. Yossi Tsfadia Tel Aviv University Faculty of Life Sciences Tel: 3-972-6405766 Fax: 3-972-6405146 E-mail: [EMAIL PROTECTED]
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