I based my comment on this reply from Thomas Cheatham III, on Sep, 19. I've
also performed some tests and realized that for ptraj the mask is static
and does not select different atoms each frame.
However I haven't tried cpptraj.
Also the manual suggests to don't use "closest" with diffusion, as the
molecule numbers are not preserved, and I would guess it messes up the
statistics.
In this way, I've just done diffusion for the bulk system, and the results
are very accurate for this case.
On Tue, Nov 1, 2011 at 12:19 PM, 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.
>
> 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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> > --
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> > Bruno Barbosa Rodrigues
> > PhD Student - Physics Department
> > Universidade Federal de Minas Gerais - UFMG
> > Belo Horizonte - Brazil
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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 - 08:00:05 PDT
