AMBER Archive (2009)
Subject: Re: [AMBER] Strange QM/MM Divcon - help me out
From: case (case_at_biomaps.rutgers.edu)
Date: Thu Aug 13 2009 - 10:52:34 CDT
On Thu, Aug 13, 2009, s. Bill wrote:
> I was trying to do simulation of a solvated protein using QM/MM
Just a question: are you sure you want to do this? It looks like your
quantum region is only 11 atoms. There is no advantage to using divcon, and
you should remember that it has been tested by fewer people than the non-divcon
QM/MM code. Plus, options like qm_pme and qm_ewald are ignored by divcon,
which may not be what you want.
> atoms, and after 3ps it stopped, becuase a part of the protein moving
You probably need to run a simulation slightly shorter than the one that
crashes, then look at the output coordinates visually, and start to figure out
what is happening.
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