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

bharat gupta bharat.85.monu at gmail.com
Sat Sep 29 14:31:45 CEST 2012


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


On Sat, Sep 29, 2012 at 9:27 PM, rama david <ramadavidgroup at gmail.com>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 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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