Dear Amber users!
I'd like to simulate water permeation into the interior of the protein in
response to the ligand binding using enhanced sampling method.
For this task I've chosen accelerated MD method with the applied dihedral
angle boost. Assuming my protein consisted of 414 residues and <DIHE>=4099
kcal/mol
I've used
iamd=2,EthreshD=4390,
alphaD=290,EthreshP=0,
alphaP=0,
/
as the result I've noticed in log the same output as
EAMD_BOOST = 3.6823
does this value corresponded to the added dihedral term of all my system or
to one degree of freedom residue ?
Also I'll be thankful if you provide me with some script suitable for
calculation of averages of all output values like dihedral energy etc
TFH,
James
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Received on Sun May 25 2014 - 07:00:02 PDT
