[gmx-users] Density measurment

Justin Lemkul jalemkul at vt.edu
Tue Oct 2 16:58:20 CEST 2012

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


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