Morteza,
In principle, any modification of the radii or well depths means that you
are no longer using the AMBER force field. Any such modifications, at least
if published, would require justification in my opinion.
There is some precedent for doing this, for example, I believe Lachele
answered an earlier post about the rare instabilities in GLYCAM. Another
instance I am familiar with is the modification of the TIP3P model with the
CHARMM force field, where the hydrogens were given the parameters of
epsilon = 0.046 and Rmin/2 = 0.2245. It is generally accepted in the
literature that this does not affect thermodynamic properties beyond the
detection of normal statistical errors.
Regards,
Brian
On Fri, Apr 19, 2013 at 6:17 PM, Morteza Chehel Amirani <
chehelam.ualberta.ca> wrote:
> Hello
>
> I need to change vdW parameter for HO-
> type atom in the system I'm studying since Gaussian can not deal with zero
> vdW parameters in MM optimization calculations. I'm just wondering what
> values I can use
> for them? I used 0.0000 0.0001 and it works. Actually, if I choose a very
> small value for epsilon the problem get fixed. I'm wondering if this
> adjustment is admissible within Amber FF calculations?
>
>
> Sincerely
> *Morteza Chehel Amirani*
> PhD Candidate
> Department of Mechanical Engineering
> University of Alberta
> 6-29 Mechanical Engineering Building
> Edmonton, Alberta, T6G 2G3
>
> http://www.ualberta.ca/~chehelam/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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radak004.umn.edu :
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Received on Mon Apr 22 2013 - 06:30:02 PDT
