Fwd: amber-developers: Re: [Fwd: input coords for REMD in Amber9]

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 8 Oct 2008 15:30:44 -0400

Hi everyone,

I'm forwarding around this patch again that fixes restart behavior
during replica runs in Amber 9. Both Holger and I have tested it now
and if no one objects I think it may be good to have on the bugfix
page. A full explanation of the problem and solution is below. If
anyone catches any mistakes definitely let me know.
Take care,
-Dan

---------- Forwarded message ----------
From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, Sep 22, 2008 at 2:36 PM
Subject: Re: amber-developers: Re: [Fwd: input coords for REMD in Amber9]
To: gohlke.pharmazie.uni-kiel.de, amber-developers.scripps.edu


Hi All,

After running my own tests I can see where the bug comes from. Amber9
REMD is a bit confusing in that even when repcrd=0 (print out
trajectories and information by temperature), restart files always
behave in a replica-specific fashion (which means among other things
that the lowest number restart file is not necessarily the lowest
temperature restart file). In multisander.f the input coordinates of
the current exchange are set to be the restart file of the previous
exchange, except on the first exchange where the input coordinates are
the ones specified by '-c'.

However, this doesn't take care of REMD run restarts; if we are
restarting the run, on the first exchange we want inpcrd to be the one
we read the temperature from, not the one with the extension that
corresponds to the temperature list. So, I just added a section that
will restore the original inpcrd that has the correct temperature on
the first exchange if irest=1. I am attaching a patch that will modify
multisander.f to do this. I have run it through the standard test
cases and it seems to work fine, but I would like Holger and perhaps
others to verify it works as well.

-Dan



-- 
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741



Received on Sun Oct 12 2008 - 05:07:27 PDT
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