From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Sat Nov 24 2012 - 09:54:46 CST
Dear */Baogen,
/*
> I want to calculate the relative free energy between RAN polymerase
> and ATP or GTP using FEP method implemented in NAMD software. Firstly,
> the mutation of ATP to GTP in water solution is calculated. After 100
> ps equilibrium of the system, forward and backward FEP analysis are
> carried out. The energy values are close when lambda value is larger
> than 0.5. But there exists deviation when lambda value is less than
> 0.5. what will result in this condition?
Who knows! What can be predicted, however, from the values assigned
toalchVdwLambdaEnd and alchElecLambdaStart is a discontinuity
of?/G/ at λ = 0.5, when only the van der Waals term of the
intermolecular interactions subsist for the perturbed portion of your
system. This aspect
of free-energy calculations is actually discussed at length not only in the
user's guide, but also in the dedicated FEP tutorials.
> The FEP parameter setting is as follow:
> alchVdwLambdaEnd 1.0
> alchElecLambdaStart 0.5
> alchVdWShiftCoeff 4.0
> alchDecouple on
> */Another question is how to obtain the energy value when lambda is
> equal to 0 or 1 corresponding to forward or backward analysis?
> /*
*//*Your question is not particularly clear. There seems to be a confusion
between /energy/ and/free energy/. Since you are running FEP calculations,
what you are measuring is not a free-energy change at λ, but a free-energy
change between λ and λ + δλ. Conventionally, in a forward free-energy
calculation, ?/G /is 0 at λ = 0. Likewise, in a backward transformation,
?/G /is 0 at λ = 1.
> */If the initial value of lambda is 0, and increment is 0.05. when the
> calculation is completed, the output *.fepout file will give the
> energy value from 0.5 to 1. /*
No. Unlike the starting point of your simulation is set to be 0.5 and
its endpoint
to be 1. I can assure you that if you usefep.tcl and write
runFEP 0.0 1.0 0.05 $nSteps
your output file will, indeed, contain all the free-energy changes from
0 to 1,
i.e., 0 to 0.05, 0.05 to 0.1, etc... 0.95 to 1.
> */Does the energy value correspond to lambda(0) state when I set the
> FEP parameters alchLambda (0 ) and alchLambda2 (0) *simultaneously?*/*
If you set concomitantly /alchLambda//and //alchLambda2to 0,/ you will
compute a free-energy change between λ = 0 and λ = 0 -- and find out
that ?/G / is 0. Computer time well spent.
> */*Would you like to help me with the problems? *
> /*
If you do not find a nil ?/G /between λ = 0 and λ = 0, please, write to us.
> */Thank you for your great help!
> /*
> */Best wishes/*
> *//*
> */Duan Baogen/*
Chris Chipot
--
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_edam.uhp-nancy.fr
Web: http://www.ks.uiuc.edu/~chipot
http://www.edam.uhp-nancy.fr
The light shines in the darkness, and the darkness has not overcome it.
John 1:5.
_______________________________________________________________________
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