AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Jun 28 2006 - 16:11:22 CDT

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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