[gmx-users] Energy minimizations with gmx3.2

[David]

On Sat, 2004-05-22 at 19:30, Alan Wilter Sousa da Silva wrote:
> Hi David!
> 
> (OT: When do you take a brake? :-)
No comment...
> 
> 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.
Force fields do have systematic errors in that the minimum energy
structure is not the same as the experimental structure. However, to
compare fair, you should perform a simulation of the crystal structure
in a crystal environment. For NMR structures you should compare to the
entire NMR ensemble and to data.


-- 
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
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