AMBER Archive (2006)

Subject: AMBER: TI-FEP : strange result for different clambda values

From: Biswa Ranjan Meher (brmeher_at_iitg.ernet.in)
Date: Fri Sep 22 2006 - 10:26:30 CDT

Dear AMBER users,
For my protein-drug system: we are doing the free energy perturbations in a
transformation of ILE ---> VAL using the TI method. We used 14 windows of
clambda value as 0.05, 0.15, 0.25........0.85 and 0.90, 0.92.....0.98 with
klambda = 6, as per the AMBER tutorial for tolune-->nothing. But
strange thing in the result is that, in the last windows of clambda value
0.90 to 0.98 we are getting the DV/DL almost zero difference. The
different clambda values and there respective DV/DL values we found are as
follows:

clambda DV/DL
0.05 50.4736
0.15 25.9430
0.25 12.2901
0.35 5.2432
0.45 1.6762
0.55 0.5597
0.65 0.1154
0.75 0.0253
0.85 0.0020
0.90 0.0002
0.92 0.0001
0.94 0.0000
0.96 0.0000
0.98 0.0000

Here is the input file for the calculation.

Transformation of ILE 2 VAL Equilibration:

&cntrl
   ntr=0,
   nstlim =20000, nscm=2000, ntave=5000,
   ntx=1, irest=0, ntb=2, ntpr=100, tempi=300.0, ig=974651,
   ntp=1, taup=1.0,
   dt=0.001, nrespa=1,
   ntt=1, temp0=300., tautp=2.0,
   ntc=2, ntf=2, tol=0.000001,
   ntwr = 10000, ntwx=0,
   icfe=1, clambda=0.96, klambda=6,
   cut=9.0,
  &end

Transformation of ILE 2 VAL production phase
  &cntrl
   ntr=0,
   nstlim =100000, nscm=2000, ntave=5000,
   ntx=7, irest=1, ntb=1, ntpr=100,
   ntp=0, taup=2.0,
   dt=0.001, nrespa=2,
   ntt=0, temp0 = 300., tautp=2.0,
   ntc=2, ntf=2, tol=0.000001,
   ntwr = 10000, ntwx=0,
   icfe=1, clambda=0.96, klambda=6,
   cut=9.0,
  &end

So can anybody please point out the mistake and suggest to overcome it. Thanks
for your suggestions.

Regards
Biswa Ranjan Meher

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