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

[Justin Lemkul]

On 9/29/12 8:27 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 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.
>

g_densmap should probably do what you need, provided you have a properly fitted 
trajectory so that you have a fixed point of reference.

-Justin

-- 
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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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