This is a feature of the implementation of rigid water molecules and
pertains to the application of holonomic constraints via SHAKE. I believe
the formulation is easier in terms of bonds than angles and both are
essentially equivalent. Additionally, the default in AMBER is use the
SETTLE algorithm, which is an analytic solution to SHAKE for the special
case of rigid triangles. I am not exactly sure why a non-zero force
constant has to be specified (although I'm pretty sure the exact value is
somewhat arbitrary), but a bond, in the topology sense, must exist in order
for the constraint to be applied.
Regards,
Brian
On Mon, Aug 26, 2013 at 5:37 PM, X Sun <egeh00.aol.com> wrote:
> Dear all,
>
> I am confused about the item HW-HW for TIP3P, in Glycam06h.dat and
> Parm99.dat, the item are both shown as "HW-HW 553.0 1.5136 TIP3P
> water". It should not form a bond between the two hydrogen atoms. What does
> this item represent?
>
> Xiaoquan Sun.
>
> 2013-08-26
>
>
>
> X Sun
> _______________________________________________
> 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
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Mon Aug 26 2013 - 14:00:03 PDT
