There isn't any velocity information stored in the trajectories so you can
consider that information gone. Here's one way to do it if you do a rerun:
According to the AMBER manual:
ntwr Every NTWR steps during dynamics, the "restrt" file will be written,
ensuring that recovery from a crash will not be so painful. In any case,
restrt is written every NSTLIM steps for both dynamics and minimization
calculations. If NTWR<0, a unique copy of the file, restrt_nstep, is written
every abs(NTWR) steps. This option is useful if for example one wants to run
free energy perturbations from multiple starting points or save a series of
restrt files for minimization. Default 500.
Thus, run with a negative NTWR, so you print out restarts (that include
velocities).
Multiply these by the atomic masses and there you go.
P.S. It's probably not worth noting but if you had a REALLY high coordinate
print frequency, you might be able to get some velocity info from the
trajectories using finite difference (which you'd have to code by hand). But
it would be so error-prone, you might as well just rerun it.
--Dan
On Fri, Apr 15, 2011 at 9:33 AM, peker milas <pekermilas.gmail.com> wrote:
> Thank you Bill,
>
> Unfortunately i didn't run my simulation with mdvel option. If this is
> the only way of having them, i need to run them again i believe.
>
> best
> peker
>
> On Thu, Apr 14, 2011 at 8:29 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >> Recently i tried to find some documentation about how i can extract
> >> momentum values from trajectory files. Unfortunately, i neither could
> >> find a documentation nor figured out a way for extracting them. I
> >> would like to ask whether there is a method for getting them or not...
> >
> > You could use mdvel (velocity) values with atomic masses.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 14 2011 - 20:30:02 PDT
