[gmx-users] Energy minimizations with gmx3.2

David spoel at xray.bmc.uu.se
Sat May 22 21:12:12 CEST 2004

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 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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