[gmx-users] Energy minimizations with gmx3.2

[Alan Wilter Sousa da Silva]

Hi David!

(OT: When do you take a brake? :-)

We have worked with others MD programmes too and it seems to happen
always.

I use Gromos96 (thus, IIRC, it happens to G87).  No matter PDB file I
took, if I did a super EM, I get visible changes.  But rama can show
better.

I use procheck.  Procheck define 4 regions:

1- Most favoured (A, B, L, red)
2- additional allowed (a, b, l, yellow)
3- generously allowed (~a, ~b, ~l, cream)
4- disallowed (white)

	 So let me show what I want to point out with next table:

	PDB	EM (emtol=100)
1-	95,6	89,9
2-	 4,4	10,1
3-	 0,0  	 0,0
4-	 0,0	 0,0

The longer EM, the lower will be rama value for 1 (increasing 2).

Ok, I think it's fine, as long as I don't have anything going to region 3
or 4.  However, anyway, I do not like this.

Cheers,
Alan

--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
São José dos Campos (SP), Brasil
www.lac.inpe.br/~alan

On Sat, 22 May 2004, David wrote:

> On Sat, 2004-05-22 at 19:04, Alan Wilter Sousa da Silva wrote:
> > But Marc and All, how is your ramachandran plot after such optimisation?
> >
> > I mean, If we do too much EM our structures (according to procheck) get
> > worse and worse.  Compare rama from your original PDB to your optimised
> > (emtol < 1 or even <10).
> What does get worse? The ramchandran plot? This seems highly unlikely,
> unless there is a serious error in the force field? Which forcefield did
> you use?
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>