AMBER Archive (2007)

Subject: Re: AMBER: Addendum: Heat capacity calculations not coming out right

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Sat Oct 20 2007 - 17:47:05 CDT

That's what I was afraid of. Don't worry, for my computations I'm using
1024 water molecules, or an equivalent number (256) of glycerols, which
gives us much larger boxes.

The idea with these simulations is to test the transferability of some of
these models as solutions mix. Both seem to do well individually to
reproduce heat capacity and density, and the right densities come out as
the two are mixed, but it remains to be seen whether some other properties
come out right.

My experience with NPT simulations is also that the check is only
done once at the beginning, but then future violations are not
prevented. If I start with a diffuse scattering of molecules that
satisfies the cutoff criterion, I can start an NPT simulation to
reduce the box size until the cutoff is violated, although things
keep running happily until I try to restart the run. Thanks for improving
this check in AMBER10!

Dave
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