[gmx-users] msd

Yelash, Dr. Leonid yelash at uni-mainz.de
Thu Sep 3 15:22:40 CEST 2009

Hello together,

i have a problem with msd. i simulate a melt of chain molecules 
consisting of 116 united atoms per chain. then i copy the box n 
times in x,y,z directions, repeat simulations and get a slightly 
different msd curves:

in the time range between 1 ps and 10 ps it flattens out decreasing 
the curvature for larger boxes and at later time (>10ps) follows at 
higher msd just parallel to the curve for smaller box. 
the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so 
if it would be the finite size effect it should already disappear, but it 
I also tried with different thermostats (sd, md with nose-hoover), 
different tau_t and also switching off the removal of com (then the 
box starts to fly after awhile) 

To check from the other side if it could be the finite size effect i 
reduce the length of the chains from 116 to 58 and the whole msd 
curve shifted up, also in ballistic regime where one can expect no 
influence of chain configuration. interesting that the shift is by factor 
of ~2 (although is not exactly): perhaps i'm just doing sth wrong!
msd was calculated for chains using: 

g_msd -mol diff_mol.xvg

is anybody aware of such things or has ideas what was done wrong?
Thanks a lot in advance for any suggestions!

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