AMBER: Thermodynamic Integration with Explicit Solvent

From: Scott Pendley <>
Date: Tue, 9 Oct 2007 15:38:03 -0600

Hello AMBER users,

I have had a long history of using thermodynamic integration under AMBER 7
using parmtops and perturbed parmtops. I have read through Ross' AMBER 9
tutorial and I am trying to modify his implicit solvent tutorial to handle
my explicit solvent needs but I am having trouble getting it to work.

First I attempted to using an TI input that worked well for me before with

   nstlim=3000000, 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, klambda=6,
   icfe=1, clambda=0.043882786,

This unfortunately, led to errors with values exceeding the vmax. Next I
tried to modify Ross' input to allow for explicit solvent and am using

   nstlim =3000000, nscm=2000,
   ntx=1, irest=0, ntpr=1000,
   tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
   ntb=0, igb=0, cut=9.0,
   ntc=2, ntf=2,
   ntwr = 10000, ntwx=1000, ntave=5000
   icfe=1, clambda=0.0034357, klambda=6,

This leads to a very strange error "Error: ifbox=2 in prmtop but angles are
not correct". I have tried the parmtop and coordinate files with a regular
MD input and they seem fine. If others have had success could they share
their input file with me or any suggestions that can help me further along
this way.

Thank you,


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Received on Wed Oct 10 2007 - 06:07:53 PDT
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