Hi Amber Users,
I am trying to calculate a heat of vaporization for
a simulation on an organic solvent. From Fox and
Kollman's paper J Phys Chem B 1998, 102,8070, they
accomplish this by running two simulations. The first
simulation is a fairly standard simulation. The
second simulation is one that has a cutoff = 0.0 in
order to calculate the contribution of internal
residue based EEL and VDWAALS energies. In Amber7,
sander is able to perform a minimization with
cutoff=0, but unable to perform an MD simulation on a
periodic box of my solvent. I do not receive an error
message, the calculation just fails. The following is
my MD input:
&cntrl
nstlim=1000000,dt=0.001,
irest=1,ntx=5,iwrap=0,
ntt=1,ntb=2,ntp=1,
tempi=300,scee=1.0,scnb=1.0,
cut=0.0,comp=20.7,
ntc=2,ntf=2,
ntpr=1000,ntwx=1000,ntwe=1000,
&end
Has anyone ran into this problem? Any suggestion on
how to get sander to run with an MD simulation with a
cutoff = 0.0?
Thank you in advance.
Karl
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Karl Nicholas Kirschner, Ph.D.
National Institute of Health Fellow
Complex Carbohydrate Research Center
University of Georgia - Athens, Ga USA
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Received on Mon May 12 2003 - 15:53:01 PDT
