Ross,
You are right; I was misattributing CHARMM behavior to CHAMBER.
Brian
On Wed, Jul 20, 2011 at 7:06 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Brian,
>
> > As for the small epsilons on hydrogen, they were a modification to
> > avoid
> > oxygens and hydrogens from overlapping in a "Coulomb catastrophe." I
> > guess
> > it would seem that algorithmic improvements would preclude this from
> > happening in modern software (maybe not in Monte Carlo simulations?)?
> > The
> > modification does constitute a fundamentally different model in the
> > literature:
> >
> > Neria, E., Fischer, S., and Karplus, M. J. Phys. Chem. 1996, 105, 1902.
> >
> > Maybe this should be mentioned in the AMBER manual?
>
> I'm not entirely sure why this should be mentioned in the AMBER manual. The
> AMBER force fields, setup through LEAP, will use the original TIP3P
> implementation (with no VDW on the H's) as far as I am aware and therefore
> relate directly to the original published TIP3P. Please let me know if I am
> mistaken here. It is the CHARMM model that is different in that they added
> small VDW to the H's when implementing TIP3P within charmm.
>
> Note though that if you use CHAMBER to convert a charmm psf containing a
> TIP3P solvated system to AMBER you will get the 'CHARMM' version of TIP3P
> since it will convert the parameters directly from the psf.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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--
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Brian Radak : BioMaPS
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Received on Thu Jul 21 2011 - 06:30:03 PDT
