[gmx-users] constrained minimization

[David Mobley]

Rob,

There *is* an option for dihedral restraints in GROMACS if that's what
you're after (not sure if you are trying to distinguish between
*constraints* and *restraints*). You can of course minimize with
dihedrals, distances, and angles *restrained*, but this is a different
thing from minimizing with *constraints* on those things. Dihedral
*restraints* are like this:

topology file:

[ dihedral_restraints ]
; i j k l            type     label  phi  dphi  kfac          power
1410 1393 1391 2610  1        0      -140  0  fc_dihed     2

mdp file:
<snip>
define = -Dfc_dihed=41.84
<snip>
dihre=simple
dihre-fc=1

David

On 1/10/06, rob yang <nextgame at hotmail.com> wrote:
> >From: David van der Spoel <spoel at xray.bmc.uu.se>
>
> >rob yang wrote:
> >>Dear list,
> >>Is there a way to perform minimizations with 1 or more torsion angles
> >>frozen? Can ffscan do it? If so, where would I find an example file on the
> >>"param.dat" file that's needed for ffscan? Thank you very much in advance.
> >>
> >Maybe you can do it by adding constraints, but only using mdrun.
> >ffscan is for force field optimization.
> >
>
> Thanks David. 2 fold questions in response to that:
> 1) unless i am missing something, there's no torsion constraints available
> (just position, angle constraints) in gromacs
> 2) i am trying to improve force field torsion parameters to suit my molecule
> better, so does that count as force field optimization? just out of
> curiocity, is there an example for using the ffscan function?
>
> thank you.
>
> rob
>
>
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