Re: [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ

From: anu chandra <anu80125.gmail.com>
Date: Fri, 5 Jan 2018 16:05:32 +0530

Thanks Daniel. I will explore the cpptraj GitHub version.

On Thu, Jan 4, 2018 at 7:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> What you want is possible, but only with the GitHub version of cpptraj
> (https://github.com/Amber-MD/cpptraj), which allows distance
> calculations using a reference frame for the second mask. You want
> something like:
>
> parm myparm.parm7
> trajin mytraj.nc
> reference mytraj.nc 1
> distance .1 @1 reference out Atom1.ref.dat
>
> Hope this helps,
>
> -Dan
>
> On Thu, Jan 4, 2018 at 6:41 AM, anu chandra <anu80125.gmail.com> wrote:
> > Hello Amber usrs,
> >
> > I am trying to calculate distance between two atoms, atomX(f1) and
> > atomX(f2-fn). Here 'atomX(f1)' is the atom X from the first frame of the
> > trajectory and 'atomX(f2-fn)' is the same atom X, but from the second
> frame
> > to the nth frame. Now I would like to calculate distance between
> atomX(f1)
> > and atomX(f2-fn) along the simulation trajectory. I wonder whether such
> > calculation possible with CPPTRAJ. I am aware of 'distance' module in
> > CPPTRAJ which calculate the distance between atoms within each frame. Any
> > suggestions would be highly appreciated
> >
> >
> > Many thanks in advance
> >
> > Anu
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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>
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Received on Fri Jan 05 2018 - 03:00:02 PST
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