[gmx-users] Rigid body optimization

Mengjuei Hsieh mjhsieh at yahoo.com
Sat Dec 6 13:24:00 CET 2003

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 :-).

It still would be great to have a rigid body code in update.c. That may help
some docking jobs easier.

Mengjuei Hsieh

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