i did some energy error analysis a while back and found this
combination to work best for me:
dt = 0.001, cut = 99.0, nrespa=4,nrespai=2,cut_inner=15.,
you might have to look at the code to fully understand these options.
On Thu, Sep 30, 2010 at 12:42 PM, David Tanner <dtanner.ks.uiuc.edu> wrote:
> David Case or other GB-OBC developer,
>
> I am very interested in using Amber's Generalized Born - OBC implicit
> solvent, but I had a couple questions about cutoffs which I hope you, or one
> of your associates, could answer for me.
>
> I am mainly wondering how you determine appropriate cutoffs (Amber Users
> Guide says cut=16Ang, rgbmax=10-15Ang or default 25Ang). Were these
> recommendations based on experiments you did, perhaps calculating error? or
> was the implicit solvent parameterized for cutoffs of 16 and 25 Angstroms?
> Any information you have on this will be very helpful in choosing cutoffs; I
> am trying to simulate a very large molecule, so knowing the shortest and
> safest cutoffs will be helpful, but knowing why is even more helpful for
> making sure my science is somewhat concrete.
>
> Thank you so much,
> David E. Tanner
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Received on Thu Sep 30 2010 - 11:30:03 PDT
