[gmx-users] g_msd and Diffusion coefficient

Yossi Tsfadia YossiT at tauex.tau.ac.il
Thu Apr 26 10:36:25 CEST 2007

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:  yossit at tauex.tau.ac.il


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