RE: AMBER: Strange behavior on g95 compile.

From: Ross Walker <>
Date: Wed, 7 Feb 2007 08:17:37 -0800

Dear Martin,

> g95 -c -O3 -fno-second-underscore -ffree-form -I../../sander -o
> ../obj/random.o ../obj/random.f
> In file ../obj/random.f:11
> FUNCTION xrandom(idum)
> 1
> Warning (139): Value of function 'xrandom' at (1) is never set
> In file ../obj/random.f:22

Please see bugfix 28 on

This should fix your problem. Remember to do a make clean in $AMBERHOME/src/
after applying it.

> Once sander has been made in this way when I run it it
> behaves very very
> oddly, for intance when simulating a box of just 375 TIP3P water
> molecules at 273 K it's first action is to drop the
> temperature of the
> simulation to ~60K and continue at that temperature.

First of all start with a fresh copy of the amber source code and apply
bugfix.all from the amber website. Then try building the code. Then cd
$AMBERHOME/test/; make and see what test failures you get. If these all work
fine or with only minor roundoff differences then the problem is likely with
your simulation protocol and more details will be required to find out what
is going on. If the tests cases fail please send us some more details
including the TEST_FAILURES.diff file from the test directory and your g95
version number, machine specs, src/config.h file etc.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Feb 11 2007 - 06:07:08 PST
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