Dear all,
Will you please tell me in which condition the
constant is 332? As we know, the microenviroment of
the biomolecule is very complex. My understanding is
that different part of the protein will have different
electrostatic energy constant, becaused some part are
much condersed with polar residues, some part are much
condensed with hydrophobic groups, and the residues
composition in each part will be the microenviroment
for the electrostatic energy calculation.
I am looking forward to getting your discussion on
that.
Best regards.
Fenghui Fan
--- Thomas Cheatham <tec3.utah.edu> wrote:
>
> > 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
>
>
-----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu
>
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 01 2006 - 06:07:20 PDT
