On 2012-03-30 13:15, Ignacio Fernández Galván wrote:
--- On Fri, 30/3/12, David van der Spoel<[email protected]> wrote:
Why are you freezing part of the system?
I want a given molecule (20 atoms) to be rigid. Is there a better way that
works for any kind of molecule (not just water)? I believe freezing it should
be equivalent to keeping it rigid and removing the center of mass motion.
The VAC looks ok doesn't it? How many molecules?
My concern is it doesn't look like the typical VAC I find in the literature (as
in<http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/vaf.html>), and I
don't know how to quantitatively analyze this function.
It looks like it is relaxing slowly from an unnatural conformation / phase.
There are 459 solvent (acetonitrile) molecules. Not too many, I know, but it's
box size of ~40 Å.
And how are you treating the linear angle?
What is the temperature of your system?
Around 295 K.
Is it starting from an equilibrated liquid?
Yes, or so I believe. I run a 50 ps equilibration first, and use the resulting
checkpoint with -t
Have you checked the diffusion constant to test whether it is liquid?
You can do that from the VACF and from the mean square displacement.
Thank you,
Ignacio
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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