AMBER Archive (2004)

Subject: Re: AMBER: sander output

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 19 2004 - 23:54:32 CST

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_at_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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