I agree with your explanation Jason. My question came from the "strange" comment added after the Ho parameters term in the GLYCAM06-h1 dat file
Best
Stephane
De : Jason Swails [jason.swails.gmail.com]
Date d'envoi : mercredi 16 janvier 2013 18:06
À : AMBER Mailing List
Objet : Re: [AMBER] LJ parameters for Ho in GLYCAM06 changes
On Wed, Jan 16, 2013 at 8:05 AM, ABEL Stephane 175950
<Stephane.ABEL.cea.fr>wrote:
> Dear all,
>
> I have noticed that the LJ values for Ho atom in GLYCAM06 have been
> changed between the GLYCAM06-h-1.dat and GLYCAM06-g-1.dat force field
> versions
>
> GLYCAM06-h1: Ho 0.2000 0.0300 M.B. Tessier 2011,
> use by permission only
> GLYCAM06-g1: Ho 0.0000 0.0000 OPLS Jorgensen,
> JACS,110,(1988),1657
>
> It is possible to have in few words a justification of this change and its
> impact in ND simulation
>
Without any VDW parameters on that hydrogen, some people were observing
occasional blowups of their simulations caused when an atom collapsed into
one of these hydrogens. The idea was that the connected oxygen's VDW
radius would be large enough to block any atom from collapsing into the
hydrogen, but sugars are tricky beasts (as the Glycam developers can well
attest).
Since 1-2 and 1-3 interactions are excluded, I think it's possible for an
atom forming a dihedral with the hydrogen (and therefore an angle with the
oxygen) to collapse into the Ho atom without ever feeling the repulsion
from the oxygen. Therefore, the solution devised was to give that H atom a
small van der Waals term. It is so small that it is virtually
non-attractive, but still has the 1/r^12 term to prevent catastrophic
collapses that blow up simulations.
I would expect no adverse affects from such a change (and this change is
probably documented somewhere, in an article maybe).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 16 2013 - 11:30:03 PST
