[gmx-users] Rigid body optimization
spoel at xray.bmc.uu.se
Sat Dec 6 14:43:01 CET 2003
On Sat, 2003-12-06 at 13:22, Mengjuei Hsieh wrote:
> on 12/5/03 11:27 AM, David at spoel at xray.bmc.uu.se wrote:
> > On Thu, 2003-12-04 at 22:06, Mengjuei Hsieh wrote:
> >> Perhaps we need constraints according to the starting structure, not ideal
> >> angles/lengths like what CHARMM does.
> > If you want to do it nicely, you'd have to sum the atomic forces over
> > the molecule and then integrate the whole molecule as a rigid body
> > indeed (with net force and torque giving exactly six degrees of
> > freedom). It wouldn't be so hard to implement, except when molecules are
> > split over processors. I assume as well it would require double
> > precision. For the sequential bit, I would gather that it would be less
> > than 100 lines of code to add in update.c
> Yes, that would be the case to treat the whole molecule as a rigid body. If
> we want to have several rigid fragments instead of a rigid body (say,
> protein), we probably need to design the constraints :-).
if you want them really rigid it will be problematic to get constraints
between the element. Say you'd want to treat the 7 helices of myoglobin
as rigid, and the links between as normal constraints. That would be
quite ugly to implement.
> It still would be great to have a rigid body code in update.c. That may help
> some docking jobs easier.
Hmm... Be my guest implementing it...
David van der Spoel, PhD, Assist. 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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