On 10/2/12 7:07 AM, rama david wrote:
Hi Gromacs Users,
I did simulation of two random coil peptides for 100ns.
after 70 ns these peptide get converted to anti parallel beta sheet
structure.
I am interested to see the water density in between these peptideswith
respect to time change
and also the no of water molecule between the peptide with respect to time.
And at the same time the distance between the peptide..
I need these information in xvg graph.
I found out the distance between peptide by g_mindist
but I not found the appropriate way to calculate density of water with
respect to time
between two peptides..
I used g_density but it not gave me the information as per my need.
There are a variety of options in g_density that might work, like changing the
direction along which the box is sliced, the interval of time examined, etc. I
can envision this working quite well. g_densmap can do similar functions, and
g_rdf can probably provide you with some useful information as well.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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