AMBER: thermodynamic integration

From: Servaas Michielssens <>
Date: Sat, 28 Apr 2007 19:48:10 +0200

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.

    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" ,
    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.
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Received on Sun Apr 29 2007 - 06:07:52 PDT
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