AMBER Archive (2003)

Subject: AMBER: FEP problem

From: Itziar Maestre Asenjo (itziar_at_qorws1.uab.es)
Date: Thu Sep 18 2003 - 07:35:37 CDT

Dear Amber users

I am running a FEP with GIBBS. I begin from one structure that has been
stabilized during 5000ps of MD simulation.
The FEP simulation runs OK and I have no error message in the output
file, but I found that in the lasts windows of the simulation the value
of the z-coordinate for my molecule is infinite, thus I cannot see my
molecule grafically with any program (I have no restart file, and the
trajectory file is not complete)

Here is the input file I am using:

Calcul FEP de 200 finestres de 100ps
Temperatura constant 300k
 &cntrl
  ntx=5, ntb=0,
  ntt=1, temp0=300.0,
  nstlim=-1,
  ntc=2, scee=1.2,
  ntpr=100000, ntwx=100000,
  almdel=0.005, isldyn=-3, nstmeq=20000, nstmul=80000,
  ndmpmc=100,
 &end

I would like to know if there is any way to solve this problem

Thank you in advance

Itzi

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