[gmx-users] NM and energy minimization

[Bert de Groot]

On Sat, 24 Jul 2004, John Simms wrote:

> Hi All,
> I would use normal mode analysis to study rhodopsin, which is a membrane
> protein.
> I have tried to EM the protein, in a vacuum, using cg in double precision,
> but cant get the Fmax
> to a level useful for NM analysis. The minimization stops at about Fmax ~
> 30, and what ever i try
> i cant get a level lower than this. Has anyone used NM on membrane proteins,
> any sucess?
> As usual any help will be gratefully accepted.
> Cheers
> John
>
>


Hi John,

Do you use cut-off's? For an energy minimisation prior to NM you probably
shouldn't.
setting pbc = none and rlist=rcoul=rvdw=0 is I think the most efficient
way to achieve  this  (otherwise set the cut-off radii to a large enough
value that it includes the whole protein). Also, check the archive, as
this issue has been discussed a couple of times already IIRC.

If you're unlucky, there is no local minimum (in vacuum) near the
structure you started from, and minimising until you reach a "proper"
minimum would in such case lead to a transition to a potentially
artificial configuration. If that happens, you might want to add
(part of) a realistic surroundings, like e.g. a solvent/lipid layer.

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________