[gmx-users] Rigid body optimization

David 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...

> Best,
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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