[gmx-users] special molecule
hotafin at gmail.com
Tue Jun 13 13:12:52 CEST 2006
Does it mean, that the itp file, generated by the PRODRG server should only
used with the gmx forcefield, or may it be combined with the other gromos
frocefields, like the G43a2?
On 6/13/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Dongsheng Zhang wrote:
> > Sear Mark,
> > Since PRODRG server only generates a itp file by using gromos type force
> > field, do I have to use gromos force field for my whole protein-ligand
> > system if my ligand force field parameters are got from PRODRG? In
> > another word, can I mix two different force field (one for protein, one
> > for ligand) in one system? Thanks!
> It's technically possible, if fiddly, but I'd strongly advise against
> it. Force fields are mathematical constructs that are optimized to
> produce reasonable model physics as an interacting unit. There is no
> reason to suppose that a bond stretching parameter is a measure of bond
> strength, for example, because the other parameters in this force field
> might have some quirk that this parameter is compensating for because of
> the optimization procedure. A force field is merely a point in a
> high-dimensional space which when used the right way has been shown to
> produce a useful physical model. Thus there is no reason to suppose that
> a few of those high-dimensional space coordinates plus some others from
> some other force field will combine to produce a useful physical model.
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