On Tue, Apr 26, 2011, nicholus bhattacharjee wrote:
>
> Now the problem is that during equilibration i.e. MD I am unable to put
> larger force constant i.e. rk3>50 is not getting permission showing shake
> default. Now some of the results from the minimization is as bellow
>
> Force constant (rk3) Final distance of the restrained
> atoms
>
> 60 2.26
> 70 2.08
> 80 2.17
> 90 2.04
> 100 2.22
> 200 2.02
> 300 1.99
> 400 1.94
> 500 1.75
> 1000 1.83
> 5000 1.63
Seems to me that this is exactly what you should expect to see. For a force
constant of 60, the penalty for a 0.26 Ang violation is 60*(.26)**2 =
4kcal/mol. If there are other forces that are driving the distance to be
large (and it looks like there are), then this might represent a balance of
forces.
Amber distraints are not "hard walls", and are primarily intended for use with
MD. SHAKE failures at rk3=50 are surprising: try running with dt=0.001.
...dac
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Received on Tue Apr 26 2011 - 07:00:03 PDT
