Yanmei Song wrote:
I did not develop the force field of my molecule by myself. In stead I
use the literature force field parameters. I guess not all the force
field need the [pairs]. As long as I can get reasonable experimental
observables, I can use such force field, right?
No. Magically getting the right answer from an unsound model does not make the
model right. I looked into that reference you provided before; these parameters
have little or nothing to do with any sort of Gromos force field, which is what
PRODRG tries to give you (and which I assume you are then using). The nonbonded
interactions derived in the paper are of Buckingham type, but the default
function type for Gromos96 is standard L-J. Furthermore, the derivation scheme
used (ab initio geometry and charge calculations) has no relevance to the
Gromos96 derivation scheme (replication of thermodynamic data in the condensed
phase).
Just because you can delete some arbitrary section and make a given parameter
more palatable doesn't mean you should do it, as Mark made quite clear. You
have to understand the intrinsics of the force field (i.e., read the original
literature) and derive parameters in the same fashion. As you've been advised,
this is a very advanced topic. It may take months or years to derive parameters
for a new species, to which I can attest personally!
-Justin
On Tue, Jan 26, 2010 at 6:50 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
----- Original Message -----
From: Yanmei Song <[email protected] <mailto:[email protected]>>
Date: Wednesday, January 27, 2010 10:58
Subject: Re: [gmx-users] Potential Energy
To: [email protected] <mailto:[email protected]>, Discussion list for
GROMACS users <[email protected] <mailto:[email protected]>>
> Dear Justin:
>
> I finally figure out that the problem comes from the Coulomb 1-4
interactions defined by [pairs] part. When I remove this parts, the
energy minimization ends with a big negative number. Thanks for your
help.
That's not a solution, that's a random number generator. Whether or
not you need such pairs is force-field dependent. Ad hoc changes are
ridiculous. Messing with force fields is an expert topic, and
parameterizing a new molecule is difficult and risky.
Mark
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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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