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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Received on Wed Jul 20 2011 - 16:30:03 PDT
