Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 7 Apr 2013 08:56:39 -0400

On Sat, Apr 6, 2013 at 4:38 PM, Diego Javier Alonso de Armiņo <
diegoarmino.gmail.com> wrote:

> Is there a way to make pmemd.cuda print distances (between atoms) to a file
> for every MD step without having to print the whole structure?
> I was thinking to put a restraint (as in umbrella sampling) with cero force
> constant and set nmropt=1, and
>
> &wt TYPE='DUMPFREQ', ISTEP1=1 /
> &wt TYPE='END' /
> DISANG=dis.RST
> DUMPAVE=x.dat
>
> plus the restraint file defining the (null) force constants and atoms
> between which the distance should be measured.
>
> Is there a more "legal" alternative?
>

This is the only way I am aware of (I am pretty certain there is no other
way).

HTH,
Jason 

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Apr 07 2013 - 06:00:05 PDT
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