Re: AMBER: sander output

From: Dave S Walker <dswalker.darkwing.uoregon.edu>
Date: Fri, 20 Feb 2004 13:47:24 -0800 (PST)

David,
        Turns out I forgot to enclose the call to corpac() with an
if(master) statement when I modified runmd(). Upon doing so the problem
was resolved. Thanks for your help.

dsw

On Thu, 19 Feb 2004, David A. Case wrote:

> On Thu, Feb 19, 2004, Dave S Walker wrote:
>
> > 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.
>
> I'm not sure how this could be happening. As far as I can see, the call
> to corpac() in runmd() [which writes to unit 13] is inside an "if (master)"
> block, and so will only be executed by the master node. Does this file go
> away with just one node? Get bigger as the number of nodes gets bigger?
>
> Since you clearly know you way around the code, you should be able to
> track down most of these things youself.
>
> ...good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case.scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri Feb 20 2004 - 21:53:01 PST
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