Re: [gmx-users] Calculate Density with respect to time...

[rama david]

Thank you for your immediate reply..

I need the xvg graph that will tell me the density of water in between the
protein with respect to time .
g_densmap not give such out put..

Sol please would you tell me  how to do it ???

How to select the Sol that  are only in between the protein ??


Thank you in advance..


With best wishes and regards

Rama David
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Re: [gmx-users] Calculate Density with respect to time...

[bharat gupta]

Hi,

There's a plugin in VMD called volmap which I think can be used for this
kind of analysis.



Bharat


On Sat, Sep 29, 2012 at 9:27 PM, rama david ramadavidgr...@gmail.comwrote:

 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 peptides w.r.t.
 to time change
  And at the same time the distance between the peptide..

 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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