[gmx-users] Rigid body optimization
mjhsieh at yahoo.com
Sat Dec 6 13:33:00 CET 2003
on 12/5/03 12:17 AM, Anton Feenstra at feenstra at chem.vu.nl wrote:
> Mengjuei Hsieh wrote:
>> 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.
> First off, all-angle constraints will fail with LINCS, LINCS cannot handle
> that type of contraints at all.
> Second, it wouldn't be too hard to write a script that parses out all
> relevant constraint pairs (i.e. for bond and angle restraints), gets
> the appropriate actual distances from your starting conformation, and
> writes that back into your topology as the constraint distance.
You are right about the LINCS and angle constraints, it is also written in
the manual. The thing is, for a system larger than small molecules, SHAKE
doesn't work very well either.
Anyway, thanks. I learned something today, the topology would be a very good
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