[gmx-users] Rigid body optimization

Mengjuei Hsieh mjhsieh at yahoo.com
Thu Dec 4 22:07:01 CET 2003


I want to confirm that the all-angles constraints in gromacs is almost not
usable. I tried lots of times trying to figure out. The problem might be
related to whether or not the starting structure is built with ideal
geometries. This might not be a bug, but a feature instead. Angle
constraints are very complicated and very hard to iterate to reach under the
tolerance if we use SHAKE/LINCS algorithm.

Perhaps we need constraints according to the starting structure, not ideal
angles/lengths like what CHARMM does.

Any idea?

Mengjuei Hsieh

on 12/4/03 12:15 AM, Anton Feenstra at feenstra at chem.vu.nl wrote:
> constraints = all-angles is not often used, so you may have stumbled on
> a bug here. Could anyone confirm whether all-angles constraints still
> works (and with which FF's it works), or confirm that it indeed is shaky?
> Another thing is that this does *not* make your protein really rigid,
> just more rigid than it normally would be. There is no proper 'rigid body'
> constraints algorithm implemented in Gromacs...

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