[gmx-users] msd

Berk Hess gmx3 at hotmail.com
Thu Sep 3 16:44:07 CEST 2009


g_msd calculates the msd for molecules, not for atoms.
I guess that would explain the result when you half the chain length.
It might also explain the box size effects, since whole chains will
still have a reduction in MSD due to periodiciy with a box of 3 Rg.

If you run g_msd without -mol you get the MSD per atom.


> From: yelash at uni-mainz.de
> To: gmx-users at gromacs.org
> Date: Thu, 3 Sep 2009 15:22:40 +0200
> Subject: [gmx-users] msd
> 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 
> doesnt.
> 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!
> Regards,
> Leonid
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