Hi,
On Tue, Nov 1, 2011 at 10:19 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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.
Ptraj will accept a distance criterion in a mask and will base it on
whatever coords are defined by the 'reference' command I believe, but
will not dynamically update the mask.
Cpptraj does not make use of distance criterion except when using the
'mask' action; for 'mask' the atom mask is dynamically updated and you
can print out a list of atoms that are selected by the mask. However,
this does not change the state (since it would require modification of
the parm at every step).
-Dan
>
> 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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>
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--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue Nov 01 2011 - 08:00:07 PDT
