[gmx-users] Re:trestart

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 30 11:41:46 CEST 2009

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.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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