Sunil Thapa wrote:
Respectable Justin/David/Mark and all other Experts
Grettings
I am not clear about the function of the option -trestart in g_msd
With trestart =0 the msd curve is very kinky which really improves to a smooth
one when trestart=1 is set. But when I increase the value to 10, 20 and 100 ps
the smoothness of the curve is lost again.
In one article MD STUDY OF DIFFUSION OF FORMALDEHYDE ON ICE which did not use
GROMACS, there was this term -tresart which was used to take the average of MSD
curve itself by dividing it into the components of timeslots specified by
trestart. Is g_msd doing that impicitly with the value of -trestart.
Please help me out. There is not much information about it in the gromacs user manaul.
g_msd -h
Sunil Kumar Thapa
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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