[gmx-users] Re: Re: Size of perturbed groups in FEP

David Mobley dmobley at gmail.com
Tue Jan 17 19:58:29 CET 2006


About the rate of change... I recommend *not* doing time-dependent
calculations. See my exchange with Maik Goette on this subject on here just
a few minutes  ago. The literature suggests these tend to be pretty
hysteretic. Instead, run simulations at specific lambda values where lambda
modulates between your original system and your final system. Then you can
do error analysis at each of these lambda values to try and get an estimate
of how long you need to run (i.e. how long to extend your simulations by) to
get within the error you want. Probably a good starting length is >1ns at
each lambda value (after equilibration).

You can use thermodynamic integration or Bennett Acceptance Ratio (which can
be applied by postprocessing your data with mdrun -rerun) to combine your
runs at each lambda value into an estimate of the overall free energy


On 1/13/06, Bruce Milne <bfmilne at ff.up.pt> wrote:
> Hi,
> Thanks everyone for your answers. I think I understand the point about
> correlation times possible being long for FEP of D-/L-amino acids in
> small peptides (these would be octapeptides) as there are significant
> intra-molecular interactions with the side-chains that influence the
> conformation of the molecule - if the system is perturbed from D to L
> configuration a conformational change would be expected and this would
> have to be allowed to stabilise into a new conformational potential well.
> Also, when perturbing large bulky groups, more time would be needed for
> rearrangement of solvent as the group's interactions with it
> grow/shrink. So because of both of these points a long simulation with
> slow rate of change of the perturbed group(s) would be best - am I right?
> Thanks again,
> Bruce
> --
> Dr. Bruce F. Milne PhD
> Faculdade de Farmácia
> Universidade do Porto
> Rua Aníbal Cunha - 164
> 4050-047
> Porto
> Portugal
> email: bfmilne at ff.up.pt
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