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