[gmx-users] about position restrain
mailmd2011 at gmail.com
Fri Aug 19 22:16:30 CEST 2016
thanks for the advice.
The are plenty of paper have discussed that it is necessary to restrain
the backbone ,or at lease the CA atoms, of a homology models. Otherwise
it would turn out to be something completely nonsense.
Probably restrain the secondary structure would be reasonable. May I ask
how can we do this in Gromacs? Is there any documentation?
Thx a lot
On 08/19/2016 09:32 PM, Justin Lemkul wrote:
> Why is it necessary to impose any restraint on the backbone in the
> first place? If you don't have confidence in the homology model and
> you are enforcing a given structure, then there is little confidence
> that any observed dimerization is legitimate. You should prove that
> the structure is reasonable/stable and do a normal simulation without
> If, for some reason, you must apply restraints to maintain some
> secondary structure element(s), then use dihedral restraints, not
> position restraints.
More information about the gromacs.org_gmx-users