I think the code works like this (correct me if I'm wrong)
You define a mask, e.g., 3A from the solute. Then these molecules which are
within this region at the 1st frame are labeled to calculate the diffusion.
But they will fly away at the course of the simulation.
So you will end up with a diffusion value for a molecule that was within 3A
at the begin but certainly won't be there later on. I've tested many masks
for my system, DNA in water, and no matter how thin I define the mask from
the solute, I still get the bulk value, which is incorrect, as diffusion is
much smaller closer to any molecule.
Do you think cpptraj can overcome this problem and re-label the molecules
every frame?
On Tue, Nov 1, 2011 at 12:41 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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--
--
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 - 08:00:08 PDT
