[gmx-users] Re:trestart

Sunil Thapa mephysik at yahoo.com
Thu Apr 30 11:34:21 CEST 2009

Respectable Justin/David/Mark and all other Experts

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. 

Sunil Kumar Thapa


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