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Hello Jie-rong--
>
> Another question: in order.py, the force constant of ANGL and IMPR are
> ramped by
> MultRamp(ini_ang,fin_ang,"potList['ANGL'].setScale(VALUE)")
> MultRamp(ini_imp,fin_imp,"potList['IMPR'].setScale(VALUE)")
> How do these set values (k_ang and k_imp?) work in the calculation?
>
> In the old fashion, it looks like:
>
> command("""
> constraints
> inter = (resid 1:76) (resid 1:76)
> weights * 1 angl %f impr %f vdw %f end
> end""" % ( k_ang, k_imp, scaleVdw) )
>
> Does it do the same thing in order.py?
for angles and impropers, these do the same thing. The nonbonded
interactions also has to be properly configured, and this can get tricky
if you have multiple conformers within a Simulation.
best regards--
Charles
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