AMBER Archive (2006)

Subject: AMBER: remlog option changed in amber9?

From: Alik Widge (
Date: Wed Jun 28 2006 - 14:36:47 CDT


I'm testing out the AMBER9 multisander REMD code using the Pittsburgh
Supercomputing Center's machines, and I've noticed something odd. The
manual states that I can write the exchange log to a file other than
"rem.log" by using the command-line option
   -remlog [alternate log file]
to the instance of sander that I invoke from the shell.

In practice, when I do this, it seems to be ignored and the output goes to
rem.log. I've found this to be true both on the Cray XT3 (BigBen) and on
the TCS HP Alphaserver (Lemieux) systems. I notice that a couple other
things have changed from AMBER8 to AMBER9 and that the manual's not quite
perfect (for instance, page 166 gives an example that clearly is missing
some options).

So, my question: has the way of specifying an alternate log changed
between AMBER8 and AMBER9? And if it has not (i.e., the PSC compilation is
just behaving weirdly), can someone please provide guidance about what I
can tell the software maintenance gurus to help them investigate the


Alik Widge
Carnegie Mellon University

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