[gmx-users] Potential Energy

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 27 18:55:02 CET 2010

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 

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!


> On Tue, Jan 26, 2010 at 6:50 PM, Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
>     ----- Original Message -----
>     From: Yanmei Song <ysong30 at asu.edu <mailto:ysong30 at asu.edu>>
>     Date: Wednesday, January 27, 2010 10:58
>     Subject: Re: [gmx-users] Potential Energy
>     To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
>     GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>      > 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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