[gmx-users] msd

[Dr. Leonid Yelash]

Hello together,

i refer here to the problem with msd mentioned at the beginning of 
September (see also below): i calculate msd this time for monomers 
(not for molecules as before) and i still observe finite size effects 
for chains if they include fixed bonds ([constrains]), however this 
effect disappears when i replace fixed bonds by lj+fene bonds. 
Is it possible that lincs changes (slightly) the velocity field and 
hence the dynamics?

Regards,
Leonid


Berk Hess wrote:
> Hi,
>
> 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.
>
> Berk
>
> > 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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