AMBER Archive (2006)

Subject: AMBER: problem with the output file for free energy perturbation calculation

From: brmeher_at_iitg.ernet.in
Date: Mon Jan 09 2006 - 23:15:30 CST

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



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