[gmx-users] Density measurment

rama david ramadavidgroup at gmail.com
Tue Oct 2 13:07:33 CEST 2012

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
 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.

Is there any way to solve these problem.

Thank you in advance..

With best wishes and regards..

Rama david..

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