[gmx-users] Energy minimizations with gmx3.2

David van der Spoel spoel at xray.bmc.uu.se
Sun May 23 08:17:58 CEST 2004

On Sun, 2004-05-23 at 02:01, Alan Wilter Sousa da Silva wrote:
> I have done what you said to NMR (PR-HIV PDB 1BVE).  And that was fine 
> (~70% in region 1).
> I can also say that, no matter degree of optimisation, average rama 
> throughout trajctories (after termalisation etc.) converges to 70%, 
> being the original PDB a crystal (which usually start from >90%)  or NMR 
>   (already around 70%).
That's quite interesting. Maybe you should compare these results to the
paper by Alan Mark's group where they compare simulations starting from
crystal structures to those starting from NMR structure. Nevertheless I
wouldn't put too much value into this one measure of quality.

> PS: I'm wondering if you'll see this e-mail during Sunday dawn :-)
No way, dawn is at 4:00 am here

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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