On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote:
Dear gromacs users,
I have done several simulations with small lipophilic, molecules
diffusing into a DMPC bilayer.
I would like to calculate the diffusion coefficient of the molecules
inside the membrane, and therefore I looked at g_msd. The manual
(version 4.0) states on p. 250 (manual pages) that g_msd uses the
Einstein relation. Reading "Molecular Modelling: principles and
applications" 2.ed. by Andrew Leach it is explained that the "for
calculating the diffusion coefficient the mean-squared distances
should not be limited by the edges of the periodic box. In other
words, we require a set of positions that have not been translated
back into the central simulation cell." This makes sense since I try
to calculate the distance a molecule diffuse.
I haven't been able to find any mention of how gromacs handle this
either in the manual or on the wiki page. The search function on the
old webpage directs me to the new webpage, which doesn't give any
results for "g_msd" or "diffusion coefficient" or alike, so my
apologies for asking a question I could have found the answer to I
old emails. When I google I get some of the old emails on g_msd from
the gromacs website, but I can only read some of them (the others
direct me to an empty page in the new webpage).
The first question is whether I can use my .xtc file made with this
command from the original .trr file:
trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc
whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting and
centring the DMPC group is used)
I would guess I could not, but should I then do the command again
creating a new .xtc file, but without using -center and -pbc whole?
You are right. You can not use this trajectory. The fitting procedure
will alter the diffusion of the system overall.
If you had to do something it would be to use -pbc nojump to allow the
molecules to freely diffuse.
g_msd takes care of the periodicity of your system. So you do not have
to fit or anything.
My second question is why g_msd has the option -rmcomm to remove COM
motion? How is g_msd created so that the diffusion coefficient can
be calculated if COM motion is removed?
The removal of the center of mass of the ENTIRE system is necessary
before calculating the msd.
This is generally done during the run using options in the mdp file.
Which version you are using? I'd never seen the -rmcomm before? You
can try to determine your
msd with and without the option and see if it affects your result.
This would depend on the removal
or not of the COM motion in your simulation.
XAvier.
Thank you very much for your time,
Sarah
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