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Dear Amber developers and users,
I am learning how to use sander to carry out free
energy perturbation calculations from the tutorial " Thermodynamic
Integration calculation using SANDER" in a Linux machine with
AMBER-7.
First, I entered xleap and edited the PHE residue to remove the
backbone and create toluene and then created the off files , prmtop and
prmcrd files. Then I run the simulation for the charging calculation in
vaccum using the input file as follows:
neutralize toluene
&cntrl
ntr=0,
nstlim =100000, nscm=2000,
ntave=10000,
ntx=1, irest=0, ntb=0, ntpr=200,
dt=0.001,
nrespa=2,
ntt=1,tempi=0, temp0=50, tautp=2.0,
ntc=2, ntf=2,
tol=0.000001,
ntwr = 10000, ntwx=0,
icfe=1, clambda=0.5,
&end
and it worked and gives the correct output
file.
But problem remains with that when I run the simulation for
the charging calculation in water using the input file for equilibration
and production respectively, the job is running for a longer period and
giving a blank output file only.
The input files are
1) for equilibration
neutralize
toluene
&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=0.11270,
cut=9.0,
&end
2) for production
neutralize toluene
&cntrl
ntr=0,
nstlim =20000,
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=0.22170,
&end
I am not getting my mistake . Can anybody please point
out the mistake and rectify it.
Thanks
Meher