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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Received on Thu Sep 18 2003 - 14:53:00 PDT
