Annette and He,
Could you let us know a bit more about your systems? How large are your
systems? Are they solvated in water?
Best,
Ray
> Dear David,
>
> Thanks for the response!
> Yes, the perturbation file and everything is created ok (I have run
> the same thing using gibbs FEP and then it works i.e. free energies
> are calculated).
> Now I just want to try it out with TI in sander and TI in gibbs.
>
> This is the gibbs FEP input that I use:
> &cntrl
> dt=0.002,
> ntx=7,
> ntpr=100,
> temp0=300,
> ntt=5,
> tautp=2.0,
> ntb=2,
> ntp=1,
> ntc=2,
> ntf=2,
> nsnb=5,
> scee=1.2,
> scnb=2.0,
> nstlim=2000,
> nstmeq=1000,
> nstmul=1000,
> intprt=1,
> nrun = 21,
> almda = 1.0,
> almdel = 0.05,
> isldyn = -3,
> &end
>
> And I would want to have a corresponding TI input (for gibbs and one
> for sander) for comparison.
> Thanks in advance!
> /Annette
>
>
>
>>>> Dear Amber users,
>>>> I want to use thermodynamic free energy calculations,
>>>>
>>>> I read the manual and try a system like this
>>>>
>>>> nstlim=1000,ntpr=100
>>>> icfe=1,
>>>> clambda=0.5,
>>>> klambda=4,
>>>> ntb=0,
>>>> temp0 = 300.0, tautp = 1.0,
>>>> ntf = 2, ntc = 2,
>>>> dt = 0.002,
>>>> ntave = 25,
>>>>
>>>> But it seems it does not calculate the free energy.
>>>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
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Received on Tue Nov 02 2004 - 16:53:01 PST
