[gmx-users] Energy minimizations with gmx3.2
spoel at xray.bmc.uu.se
Sat May 22 23:52:53 CEST 2004
On Sat, 2004-05-22 at 19:30, Alan Wilter Sousa da Silva wrote:
> Hi David!
> (OT: When do you take a brake? :-)
> We have worked with others MD programmes too and it seems to happen
> 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
> 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 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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