Re: Fw: Calculating Free Energy Change

From: Jérôme Hénin (
Date: Fri Apr 23 2004 - 16:07:52 CDT

> Hi,
> You are right! There are no FEP files for the conformational free energy
> calculations :P I think I got mixed up with the alchemical stuff.
> So if I understand you correctly, I need to specify a set of restraints
> that determine how my molecule will be 'perturbed'.
> What I have right now is the original and perturbed coordinates only. I
> don't know what kind of forces or restraints would be necessary for the
> molecule to perturb from the original conformation to the final
> conformation?? Is it possible to use NAMDs free energy calculator for
> conformational perturbations in such a way if all you know are the original
> and final coordinates?? I was reading the user guide and I wonder if
> stating values for the bound specifications might achieve this (in which
> the value of hi = (x,y,z), is the x,y,z coords of the perturbed
> conformation (see below)?? To me it doesn't sound quite right though...
> If the molecule is large, then the forcing constraints will be huge (since
> each atom has a hi x,y,z bound constraint) and NAMD does not like this...

Exactly. You can't afford to define one restraint per atom. But what you can
do is choose key-atoms or atom groups, on which the restraint will be
applied, so that these atoms induce the conformational change in the whole
molecule. Now that choice depends on your system and the nature of the


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