[gmx-users] g_msd query

Erik Marklund erikm at xray.bmc.uu.se
Thu May 19 12:02:24 CEST 2011

Anirban Ghosh skrev 2011-05-19 11.58:
> Hi ALL,
> I am trying to calculate the lateral diffusion coefficient of a 
> protein in a bilayer (CG simulation using MARTINI FF). The simulation 
> length is 5 micro-seconds. I wanted to know based on what should i set 
> the values of -beginfit and -endfit and also the value for -trestart. 
> Is it necessary to set -trestart?
> Thanks a lot in advance.
> Regards,
> Anirban
-trestart is in principle not necessary, but will provide better 
statistics. It will also increase the calculation time. -beginfit and 
-endfit should be set to exclude non-linear (non-converged) part of the 
msd plot.

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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