Re: [AMBER] Bug in nmode

From: David A Case <case.biomaps.rutgers.edu>
Date: Fri, 28 Oct 2011 09:51:21 -0400

On Fri, Oct 28, 2011, Ake Sandgren wrote:
>
> The "pointer" variables in nmode/pointer.h and variables used for
> calculating memory in alloc.f need to be integer*8.
> They are very easy to overflow at the moment.
>
> One of our users first test case was hitting this, getting memusd_x to
> end up being -1299477453...

You are welcome to make the change, but I suspect that you will be
disappointed. nmode was written in the 1970's and designed for systems with a
few dozen to a few hundred atoms. It does not make attempts to be especially
efficient with memory. You would probably be better off working with the
nmode() function in NAB. There may still be problems with systems of tens of
thousands of atoms, but at least you are dealing with a modern code, that is
parallelized and handles GB.

....dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 28 2011 - 07:00:03 PDT
Custom Search