On Tue, Jul 08, 2003, Peter Anderson wrote:
>
> I am trying to perform an entropy calculation using
> the mm_pbsa command and I'm encountering memory
> problems. I enter the mm_pbsa.pl command, some
> calculations with sander work fine for about a minute,
> and then an nmode calculation begins and quickly
> fails. The bottom of the resulting "nmode_lig.1.out"
> file reads:
>
> Total memory required : 15425318 real words
>
> Total memory avail : 3500000 real words
>
> Total memory required : 71522 integer words
>
> Total memory avail : 4000000 integer words
>
> Maximum nonbond pairs 3928477
> increase the real memory by 11925318 words
You need to edit sizes.h in nmode to increase MAXMEMX, then recompile,
and try the nmode calculations (probably just by hand at first, or on a
one snapshot "trajectory") to make sure everything is working. The nmode
program is not set up for parallel execution: this limitation has nothing
to do with the mm_pbsa script.
...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
==================================================================
Received on Wed Jul 09 2003 - 02:53:00 PDT
