On Tue, Nov 1, 2011 at 10:39 AM, Bruno Rodrigues <bbrodrigues.gmail.com>wrote:
> 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.
>
If you want the molecule numbers to be preserved, then a static mask is
exactly what you want, right? It did seem strange that someone wanted to
calculate diffusion properties with a dynamic mask (since I don't think
that's the correct way to do it, as you've pointed out).
All the best,
Jason
>
> 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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> > > --
> > > --
> > > 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 01 2011 - 08:00:06 PDT
