AMBER Archive (2004)

Subject: Re: AMBER: sander output

From: Dave S Walker (dswalker_at_darkwing.uoregon.edu)
Date: Thu Feb 19 2004 - 17:55:59 CST

Hi all,
        Using sander, I've been trying to run some liquid simulations
where I route the force array into the "ntwv" option (instead of
velocities, see below). Whenever I send output into this array I produce
a file: "fort.13", of the same size as the mdvel file (which also gets
produced). Does anyone know what it is and how its created? I suspect
that it's involved somehow with mpi but I'm not sure. Any feedback would
be greatly appreciated. Thanks for your time.

dsw

On Thu, 4 Dec 2003, Dave S Walker wrote:

> Hi all,
>
> Thanks for your help thus far.
>
> So, I've managed to route (what I think is) the force array, F, into the
> velocity output file (when ntwv>0) prior to getting them replaced by the
> "old" positions (step 3 in runmd.f). Is it safe to assume that the units
> for these values are based on the internal units, kcal/(mol x angstroms)?
>
> dsw
>
> On Mon, 1 Dec 2003, Carlos Simmerling wrote:
>
> > I think you want corpac(), called from runmd and
> > located in dynlib.f
> > Carlos
> >
> > ----- Original Message -----
> > From: "Dave S Walker" <dswalker_at_darkwing.uoregon.edu>
> > To: <amber_at_scripps.edu>
> > Sent: Monday, December 01, 2003 9:04 PM
> > Subject: AMBER: sander output
> >
> >
> > > Hi all,
> > > I'm trying to locate the code that generates the output into the
> > > mdcrd and mdvel files in sander. Does anyone know which file/files I need
> > > to explore? Any help would be greatly appreciated.
> > >
> > > dsw
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