[gmx-developers] position restraints, Jarzynski, and virial

Berk Hess hessb at mpip-mainz.mpg.de
Mon May 29 08:58:59 CEST 2006

David Mobley wrote:

> Dear all,
> So, I am trying to come up with an easy way to implement time
> dependent position restraints so that I can use the Jarzynski approach
> to do some fast-switching calculations. Actually, what I have in mind
> is to begin with a protein restrained to a particular structure, and
> then turn off the restraints in a time dependent manner and use the
> Jarzynski approach to compute the free energy for doing this. But
> that's all really beside the point here -- basically, all you need to
> know is that I want time dependent position restraints.
> It seems to me that the easiest way to do this would be to use the
> fact that lambda can already be time-dependent, and just add an input
> flag that makes this time-dependent lambda be used as a prefactor for
> the position restraint spring constant. Does this sound reasonable, or
> is there another way that is obviously better/easier?

This is already implemented.
If you look in the manual you can see that the position restraint force 
as well as reference coordinates can be perturbed.


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