OK, thanks
On Fri, Sep 5, 2014 at 2:09 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> 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 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
> > > _______________________________________________
> > > 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)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Sep 05 2014 - 11:30:03 PDT
