[gmx-users] g_msd and MSD analysis
Mr Bernard Ramos
bgrquantum at yahoo.com
Sun Jun 10 00:33:37 CEST 2012
I have a 20 ns simulation (2fs timestep but coordinates saved every 0.2 ps) and I was able to calculate the mean-square-displacement of the oxygen atoms of my water solvent. The entire MSD plot looks very linear to me. I need to fit this set of MSD data to obtain the diffusion coefficient. However, I am not sure if I will have to use the entire MSD points or may be just to consider a few picoseconds at the latter part of the simulation time. In papers I have read, they use up to a 100 ps, although no mention were made as to where those set of points came from. Please help.
This post seems to suggest a nanosecond window for the analysis of the MSD curve
Although, this other one suggests using the latter 40 ps of his MSD
Your help is greatly appreciated.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users