Re: [gmx-users] Density measurment

[Justin Lemkul]

On 10/3/12 12:22 AM, rama david wrote:

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.



I suggested before that you could perhaps advantageously using the -b and -e 
flags to achieve something similar.  You cannot get density over time per region 
of the box automatically.  That would be some sort of 3-D graph since there are 
two quantities effectively being analyzed.



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 )..



The colorized plot from g_densmap can tell you quite a lot, in my opinion.

What about g_rdf?  Integrating an RDF plot will tell you how many solute 
molecules are present in a particular region of space.  Otherwise, you can also 
use g_select to determine how many water molecules are located between your 
peptides using simple geometric criteria.  Look for examples in the archive; 
people have done this before.


-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


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Re: [gmx-users] Density measurment

[rama david]

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  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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] Density measurment

[Justin Lemkul]

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


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