[gmx-users] Density measurment

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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