Dear Dan,
Thanks for the tip, I'll give it a try.However, the command has two options
which I ignore what are they for:
<lower> Smaller distance from reference point(s). (0.01 Å)
<upper> Larger distance from reference point(s). (3.5 Å)
The documentation doesn't say anything more. I don't know what is meant by
"reference points". Any idea?
-Jose
On Thu, Sep 4, 2014 at 10:17 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Check out the 'stfcdiffusion' command in cpptraj (specifically the
> 'com' keyword), which is an alternative to the traditional 'diffusion'
> command with several advanced features. Let me know if you have any
> more questions.
>
> -Dan
>
> On Thu, Sep 4, 2014 at 4:59 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > Dear AMBER users,
> >
> > I want to calculate the diffusion MSD(t) for the center of mass of atoms
> > specified by a mask. The option 'average' in the action command
> 'diffusion'
> > does a different calculation, which is average the atomic MSD(t). I need
> to
> > first average the atomic positions (the center of mass), and then
> calculate
> > its diffusion. Is it possible with ptraj or cpptraj?
> >
> > Thanks in advance,
> > Jose Borreguero
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Fri Sep 05 2014 - 11:00:02 PDT
