[gmx-users] Density measurment

rama david ramadavidgroup at gmail.com
Wed Oct 3 06:22:52 CEST 2012

Thank you Justin for your reply ,

I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.

g_densmap have xpm output and no the xvg  ( I need density or no of water
molecule present in between two peptides  with respect to the time )..

Please, would you tell me another way to solve these problem..??

Thank you in advance

Have a nice day.
Rama David

On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==============================**==========
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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