Hi everyone,
I have introduced MoS2 to Amber and put heavy constraint on these atoms and
try to relax a 12-mer peptide on it. When I used the periodic boundary
condition in heating stage everything fell apart and peptide atoms started
to replace Mo on the surface!! I turn the periodic boundary condition off
and it is working!! I am using explicit solvation and here is the script I
am using for heating:
imin=0,
irest=1,
ntx=5,
nstlim=2500000,
dt=0.002,
ntc=2,
ntf=2,
igb=0,
ntt=3,
ig=-1,
gamma_ln=2.0,
tautp=0.5,
tempi=300.0,
temp0=300.0,
ntpr=500,
ntwx=500,
ntb=1,
cut=9.0,
rgbmax=9.0,
ntr=1,
/
constrains
1000.0
ATOM 1 3750
END
END
Does anyone know what I am missing?
Best regards,
Niloofar
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Received on Thu Jul 24 2014 - 09:30:02 PDT
