Re: AMBER: thermodynamic integration

From: David A. Case <>
Date: Sat, 28 Apr 2007 14:26:28 -0700

On Sat, Apr 28, 2007, Servaas Michielssens wrote:

> I used this as input for a free energy calculation in amber8, but in
> my outputfile their was no info of DV/DL at each step, and in de
> summary al values were 0.
> imin=0,
> ntc=2, ntf=2,
> cut=30.0, igb=2, saltcon=0.2, gbsa=1,
> ntpr=50, ntwx=50,
> nstlim = 50000, dt=0.002,
> ntt=1, tempi=1.0 temp0=300.0, tautp=5.0,
> ntx=1, irest=0, ntb=0,
> nscm = 1000, ntr=1, restraintmask=".CA,C,N" ,
> restraint_wt=1,
> icfe=1, clambda=0.04691
> I was trying to estimate te pKa of the chromophore of a GFP variant so
> I integrated between of te neutraal en anionic form.

Are you sure that the two Hamiltonians are really different? Try a one-step
run with clambda=0, and with clambda=1 to make sure you are really getting
different energies. (The behavior you report, not geting DV/DL at each
step, but still getting a summary, with all values zero, is consistent
with not having any energy difference between the two Hamiltonians.)


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Received on Sun Apr 29 2007 - 06:07:54 PDT
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