> I am wondering why in Amber, the constant used for the electrostatic energy
> computation is 332:
>
> E_el = 332 * q_i * q_j / r_ij , while in other sources this constant is
> reported as 322.0637.
This is historical. In fact, if I remember correctly, AMBER uses not 332
but 332.0522173. CHARMM uses 332.0716. The "correct" value (or at least
the one that is in my random book of tabular data) is 331.843.
To get exact agreement with energies/forces when trying to implement the
"AMBER" force fields as in AMBER, you use the 332.0522173 value. In
practice, when porting force fields most people do not pay attention to
this detail (i.e. they keep the same charges). For exact compatibility
with AMBER, in CHARMM either the charges have to be altered (i.e.
multiplied by 1.000058372 which is confusing when you read the
parameter/topology definitions especially since charges are only written
normally to the 4th decimal place!) or change the constant in the code.
In fact, you can compile up CHARMM with the "AMBER" keyword and this
constant is modified.
The effect of this modest change is likely not a serious issue, unless of
course you want exact energies and forces accurate (with PME) to the 6th
decimal place. I do not know what the value in NAMD is, but in our
experience (when run under similar conditions) the results of "AMBER" and
NAMD are virtually equivalent in terms of structure/dynamics properties
and little change is evident in CHARMM with or without the "AMBER" keyword
at compile. There is an article that trivially shows NAMD/AMBER
agreement in nucleic acid simulation: Jha et al. (2005) JCC 26, 1617-1627.
--tom
\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3.utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
http://www.chpc.utah.edu/~cheatham
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Received on Sun Oct 01 2006 - 06:07:19 PDT
