[gmx-users] about position restrain

[Albert]

Hi Justin,

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 
> restraints.
>
> If, for some reason, you must apply restraints to maintain some 
> secondary structure element(s), then use dihedral restraints, not 
> position restraints.
>
> -Justin