AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Jun 28 2006 - 16:37:54 CDT

glad that worked, and thanks for the feedback- I think
that the -remlog flag might have gotten moved after the manual
section was written.

Alik Widge wrote:

>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.
>
>Alik
>
>
>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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>
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