From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Fri Feb 18 2005 - 12:54:44 CST
Thank you so much!
However, when I ran the calculation, I met some problems. At the first step,
it was said that velocities of some atoms were faster than limitation. Then
the calculation was terminated. I had to reduce time step to 0.1 fs. Then
it could work. But it is too long to get calculation done. Do you have any
Quoting Jérôme Hénin <jerome.henin_at_uhp-nancy.fr>:
> Hi Wei,
> Derivation of the basic FEP expression shows that the kinetic contribution
> cancels out.
> Bonded terms are another problem. The FEP code in NAMD uses the (pretty
> common) assumption that their contribution is negligible.
> In the dual topology approach, the only bonded terms that would contribute to
> the free energy are those involving perturbed and non-perturbed atoms. In
> some systems, there will be no such terms (namely, when perturbing an entire
> Although I am sure one can imagine particular cases when this approximation
> make some small difference, but since the good use of alchemical FEP involves
> taking differences between free energy variations inside a thermodynamic
> cycle, most of this contribution is expected to vanish altogether.
> A good reference on that would be:
> S. Boresch and M. Karplus.
> The role of bonded terms in free energy simulations. 1. theoretical analysis.
> J. Phys. Chem. A, 103:103-118, 1999.
> Le jeudi 17 Février 2005 20:14, Wei Chen a écrit :
> > Hi,all,
> > I am using alchemify FEP in NAMD to calculate free energy difference before
> > and after mutating a residue in a peptide chain. However, I found that only
> > VDW and electrostatic energy are included in the calculation of free
> > energy. Why we do not need care about kinetic energy, bond stretching, etc.
> > Who have any ideas?
> > Regards,
> > Wei Chen
> > --
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS
> Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71
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