AMBER Archive (2006)

Subject: Re: AMBER: remlog option changed in amber9?

From: Alik Widge (
Date: Wed Jun 28 2006 - 16:24:07 CDT

It definitely does not complain on these two systems, but yes, sticking it
in the groupfile seems to have solved the problem. Thanks! (I would
suggest that maybe this should be changed in the manual, because p165
talks about -remlog in the same paragraph as -rem and -ng, both of which
are given outside the groupfile.)

The page 166 example is missing the "-rem 1" in the arguments to sander.
One can infer it pretty easily from the paragraph below (or from comparing
with the command line in the AMBER8 manual), but it's easy to miss.


On Wed, 28 Jun 2006, Carlos Simmerling wrote:

> the -remlog needs to go in the group file along with all of the other
> file specification. I thought we had made it complain if you did it outside
> but that might not work on all systems. try it in the groupfile and see if
> that resolves it- that's where I put mine.
> what's wrong with the example on page 166?
> carlos
> Alik Widge wrote:
> >Hello,
> >
> >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
> >problem?
> >
> >Thanks,
> >
> >Alik Widge
> >Carnegie Mellon University
> >
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