Re: equilibrate conf file

From: Axel Kohlmeyer (
Date: Thu Aug 16 2012 - 03:54:48 CDT

On Thu, Aug 16, 2012 at 9:56 AM, Namd Namd <> wrote:
> Dear All,
> I want to run md simulations in order to equilibrate a box of 1271 glycerol
> molecules. The box size is 47 X 47 X 70 and the target experimental density
> value I should reach is 1.261 g/cm3. Could you please suggest a conf file
> that I can change with my values and use for my glycerol simulations ?

there are a gazillion examples of conf files in the tutorials
and have been posted and discussed on this mailing list.
please have a look and help yourself to the one that seems
most suitable. i doubt if anybody has the time to do that
step for you. i also recommend to compare the choices
people make with what the documentation says about them.

please note, that equilibrium is a state where it doesn't
matter how you get there, but at the same time, it is
often very difficult to detect whether you have reached it.
this is what makes this so complicated, and a conf file
that works well in one case can be a disaster in another.
there is nothing else but careful observation and experience
that will help you here.


> Thanks for the help.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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