[gmx-users] Velocity autocorrelation

Ignacio Fernández Galván jellby at yahoo.com
Fri Mar 30 13:15:10 CEST 2012

--- On Fri, 30/3/12, David van der Spoel <spoel at xray.bmc.uu.se> 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.

There are 459 solvent (acetonitrile) molecules. Not too many, I know, but it's box size of ~40 Å.

> 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

Thank you,

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