Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass?

From: <hannes.loeffler.stfc.ac.uk>
Date: Fri, 5 Sep 2014 18:09:20 +0000

Those are only relevant when you use 'mask2' which defines a set of reference coordinates. When you choose 'com' you simple calculate the MSD for the center of mass computer from all cordinates in 'mask' (the output of cpptraj will tell you so).

________________________________________
From: Jose Borreguero [borreguero.gmail.com]
Sent: 05 September 2014 18:51
To: AMBER Mailing List; daniel.r.roe.gmail.com
Subject: Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass?

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 )
   <upper> Larger distance from reference point(s). (3.5 )
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
> > _______________________________________________
> > AMBER mailing list
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Sep 05 2014 - 11:30:02 PDT
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