Dear Amber User and developer,
I read at AMBER 10 Manual, page 37, at the desription of "cut", it is said
that "For PME, the cutoff is used to limit direct space sum, and the default
value of 8.0 is usually a good
value. When igb>0, the cutoff is used to truncate nonbonded pairs (on an
atom-by-atom basis); here a larger value than the default is generally
required."
My simulation use explicit solvent mode, so this mean igb=0 by default,
according to the manual it is enough using cutoff 8 angstrom.
I want to make sure if this cutoff only related with explicit and implicit
solvent mode ?
How about th size molecule and number of amino-acid ? is this also need to
considerate or not ?
My molecule have 388 amino acid and the size is 53.04 x 55.07 x 58.13 A
(volume total is 169792.66)
questions:
1. Is this enough to use 8 angstrom as cutoff or need larger cutoff ?
2. What is the significantly different between 8 and 12 cutoff ?
Thank you for your attention.
best regards
Setyanto Tri Wahyudi
Computational Chemistry Laboratory
Institut Teknologi Bandung - Indonesia
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Received on Mon Aug 08 2011 - 19:30:02 PDT
