[gmx-users] Density measurment
jalemkul at vt.edu
Wed Oct 3 13:07:51 CEST 2012
On 10/3/12 12:22 AM, rama david wrote:
> Thank you Justin for your reply ,
> I tried g_density again after your reply. But I found that
> it give density with respect to box dimension and not to time.
I suggested before that you could perhaps advantageously using the -b and -e
flags to achieve something similar. You cannot get density over time per region
of the box automatically. That would be some sort of 3-D graph since there are
two quantities effectively being analyzed.
> g_densmap have xpm output and no the xvg ( I need density or no of water
> molecule present in between two peptides with respect to the time )..
The colorized plot from g_densmap can tell you quite a lot, in my opinion.
What about g_rdf? Integrating an RDF plot will tell you how many solute
molecules are present in a particular region of space. Otherwise, you can also
use g_select to determine how many water molecules are located between your
peptides using simple geometric criteria. Look for examples in the archive;
people have done this before.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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