Re: [AMBER] distribution of selected water

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 Nov 2011 10:19:46 -0400

If you add distance criteria to your mask, then the mask should select different atoms each frame.

I'm not sure if ptraj has this behavior, but I'm pretty sure cpptraj does.

You can run some tests to check it out. Also, the "closest" command may help here, too.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 1, 2011, at 6:26 AM, Bruno Rodrigues <bbrodrigues.gmail.com> wrote:
> hi, as fas I know, ptraj can only do this job for the selected
> molecules using the mask. However, when you define this mask, the
> picture is static. Therefore, molecules that are whithin a certain
> region won't be there anymore in the future.
> 
> Look for this subject on the list that there is a good explanation
> exactly about this.
> 
> Best wishes.
> 
> On 10/27/11, kirtana S <skirtana4.gmail.com> wrote:
>> I want to calculate the diffusion coefficients, distribution  of selected
>> water molecules and ions, lying at a certain distance from the molecule.
>> Can I do this using ptraj.
>> 
>> Thanks in advance
>> Kirtana
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> 
> 
> -- 
> -- 
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
> 
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Received on Tue Nov 01 2011 - 07:30:06 PDT