Re: FEP simulations?

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Nov 18 2008 - 15:43:42 CST

Hi Christopher,

On Tue, Nov 18, 2008 at 2:19 PM, Christopher Hartshorn
<cmhartshorn_at_wsu.edu> wrote:
> Hello all. I have a few questions about NAMD's abilty to run the FEP
> calculations.
>
> First, can the free energy of dimerization between two molecules be
> calculated? And if so, would one make a hybrid structure that included the
> two monomers, separated in space, and the dimer (somewhere in the middle)?
> Or by some other method?

A typical way to achieve this would be to decouple one of the
molecules for the environment both in the dimer and in solution. See
e.g. this recent work:
http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/asap/abs/ct800313k.html

> Second, this is probably an obvious question but I felt I should ask before
> wasting CPU time, when I add the fep portion to my config. file (e.g. turn
> on the free energy perturbation), will all of the other values (e.g temps,
> bonded/nonbonded energies, pressures, etc.) still be output? In other
> words, does turning on the fep simply add another value that is output? And
> if so, does this increase cpu time drastically or not at all?

It does increase the cpu time moderately, depending on the options you use.

A final remark: if you are considering FEP at this point, I would
recommend to either gather the courage to try the development version
of NAMD, or the patience to wait until the next version is released,
which should hopefully not be too long now. The functionality you
would have access to is greatly improved with respect to that of NAMD
2.6.

Best,
Jerome

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