The advice you've received so far is correct -- it is important to figure
out why the calculations fail without vdW parameters on the HO atom types,
but do not fail when they are present. The GLYCAM force field parameters
are a good example of 'good' HO vdW parameters that have a minimal impact
on the 'normal' behavior. For instance, do your H atoms collapse into
other atoms in the system? It is important to understand why something bad
is happening before trying to find solutions.
Since you are using the Amber force field implemented in Gaussian, you
should find out exactly what version of the force field they have
implemented, and perhaps ask there if anybody has experienced similar
issues.
You can also look at geometry optimizations using the Amber programs to see
if you get similar behavior (although the minimizers in Gaussian will
definitely be 'better').
Good luck,
Jason
On Wed, Apr 10, 2013 at 10:27 PM, Yong Duan <duan.ucdavis.edu> wrote:
>
>
> On 4/10/13 5:22 PM, "Lachele Foley" <lf.list.gmail.com> wrote:
>
> >We had to add very small hydroxyl H vdW parameters in GLYCAM. Without
> >them, once in a while, if everything was just right, the hydroxyl H
> >could collapse onto a nearby atom with a negative partial charge (not
> >the directly bonded hydroxyl O, but some other atom nearby).
>
> If you intended to use TIP3P, SPC, SPC/E, you need to turn on SHAKE. If
> you do not turn on SHAKE, the water model is no longer TIP3P, SPC, SPC/E
> (or most of the water models).
>
> Yong
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 10 2013 - 21:30:03 PDT
