[gmx-users] how to indicate solvent flexibility?

Albert mailmd2011 at gmail.com
Thu Jan 10 11:21:27 CET 2013

On 01/10/2013 11:14 AM, David van der Spoel wrote:
> On 2013-01-10 10:45, Albert wrote:
>> Hello Justin and Leandro:
>>    thanks a lot for kind advices. I am trying to us the g_msd to
>> calculate the density:
> try g_msd -h
> wrong tool.

that's strange. Here is the information which I think it is what I want.

g_msd -h

g_msd computes the mean square displacement (MSD) of atoms from a set of
initial positions. This provides an easy way to compute the diffusion
constant using the Einstein relation. The time between the reference points
for the MSD calculation is set with -trestart. The diffusion constant is
calculated by least squares fitting a straight line (D*t + c) through the
MSD(t) from -beginfit to -endfit (note that t is time from the reference
positions, not simulation time). An error estimate given, which is the
difference of the diffusion coefficients obtained from fits over the two
halves of the fit interval.

There are three, mutually exclusive, options to determine different types of
mean square displacement: -type, -lateral and -ten. Option -ten writes the
full MSD tensor for each group, the order in the output is: trace xx yy 
zz yx
zx zy.

If -mol is set, g_msd plots the MSD for individual molecules (including
making molecules whole across periodic boundaries): for each individual
molecule a diffusion constant is computed for its center of mass. The chosen
index group will be split into molecules.

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