[gmx-developers] Re: water optimization?

Michael Shirts mrshirts at gmail.com
Fri Dec 30 07:03:00 CET 2005

Hi, Erik-

I'm working with David Mobley and John Chodera at UCSF to port my free
energy changes that I put in 3.1.4 into 3.3.  Here are some of the
things we've been thinking about -- it would be great to hear your
thoughts (and I'm cc'ing this to the developer's list to get
additional thoughts). Are there any suggestions or thoughts on these
subjects as we work on getting them in?

Here are our thoughts:

1) A toggle for decoupling versus mutating interactions of perterbed atoms.

2) Being able to print out the energy differences to arbitrary numbers
of different lambda values from the equilibrium sampled value, for use

3) Eventually, a new g_bar (or perhaps modification of g_wham) to
handle these calculations with the standard gromacs tools.

4) Evaluating the free energy only every N steps (it becomes expensive
when multiple PME calls are required)

5) A good tutorial for free energy calculations, with sample files, etc.

David, John, am I missing anything?  Anyone, any thoughts?


On 12/29/05, Erik Lindahl <lindahl at sbc.su.se> wrote:
> Hi,
> >
> > One thing I did notice is that when part of the system is perturbued
> > twice as many PME calculations are done, and grids with both the A and
> > B charges are set up.  Is this for calculating the forces for
> > decoupling of the lambda dependent part of the system, instead of
> > mutation?
> Just for dG/dl. We haven't considered only calculating it every N
> steps since it's normally 'free', but for PME it's a great idea. I'll
> try to incorporate it in the future, but if you want to you could add
> it as a 'feature request' in bugzilla, just so we don't forget.
> You're more than welcome to do it yourself too if you want, it's
> pretty straightforward.
> Cheers,
> Erik
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>     Backup address:
> <erik.lindahl at gmail.com>
> Assistant Professor, Computational Structural Biology
> Stockholm Bioinformatics Center, Stockholm University, SE 106 91
> Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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