Re: failure in RATTLE algorithm using the adaptive biasing force method

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed Nov 12 2008 - 08:43:56 CST

Hi Steve,

Actually, in this case the force constant unit is not kcal/mol/A^2 but
kcal/mol/degree^2, which is a pretty large unit. Constants of 1
kcal/mol/degree^2 or below are usually sufficient.

Jerome

> Hi Giacomo, Jerome.
>
> Thanks for your fast reply.
> I did what you've both suggested, namely checked the starting value of the
> dihedral I want to scan. The value is -163 and the first ones sampled
> during the md, before it crashes, can be read from the output as:
>
> TCL: ABF> Xi at timestep 50 : -166.472915166
> TCL: ABF> Xi at timestep 100 : -160.187081635
> TCL: ABF> Xi at timestep 150 : -162.144172289
> TCL: ABF> Xi at timestep 200 : -170.070161497
>
> So, I would suggest that a simuation in a range of e.g. xiMin=-180 to
> xiMax=0 should work. Whereas a range of e.g. xiMin=-50 to xiMax=0 should
> not, right?
> In fact, both simulations crash with the same error message.
> My next idea was to decrease the boundary force (forceConst) from 10 to 1
> kcal/mol/A^2 and now it works! Do you ave any experience which magnitude for
> the boundary force of a dihedral scan is suitable?
>
> Steve
>
>
>

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