Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field?

From: Neelanjana Sengupta (
Date: Thu Oct 30 2008 - 00:39:47 CDT


I'd like to add that NAMD2.5 would not say anything about the bond being
ignored, but NAMD2.6 actually gives out a warning message when the TIP3P
model is used. The message says something like:

Warning: Ignored 8776 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.

The system has 8776 water molecules. Please let know if this observation is


On Wed, Oct 29, 2008 at 9:37 PM, Peter Freddolino <>wrote:

> Purushottam Dixit wrote:
>> Hi,
>> If you are using SHAKE to maintain rigid water conformations (this would
>> read as 'rigidbonds water' or 'rigidbonds all'), there's a pseudo bond of
>> high spring constant between the hydrogens. Other than maintaining the
>> rigidity it has no function.
> I'm sorry, but this is slightly incorrect. If the water is kept rigid by
> rigidbonds (using SETTLE, a special constraint solver for TIP3P water) then
> the bond distances and H-O-H angle are truly constrained (ie, not allowed to
> vary at all from their equilibrium positions, and having no associated
> potential); there is no harmonic term here as a spring constant would
> indicate. The function of the H-H bond, which shows up in water prepared
> using charmm or amber, is to allow those programs to obtain proper
> geometries for the rigid water constraints; namd instead calculates the
> geometry from the O-H equilibrium bond lengths and H-O-H equilibrium angle.
> Thus, the bond doesn't generally appear in the topology files we distribute,
> and will be ignored y namd.
> Best,
> Peter
>> Purushottam
>> On Wed, Oct 29, 2008 at 11:20 AM, Ming <<mailto:
>>>> wrote:
>> Dear all,
>> I am trying to simulate my system using namd with the amber-style
>> force field.
>> Everything was fine! However I found there is a bond between the
>> two Hydrogens of
>> the TIP3P water in Amber force field. For what reason they put a
>> bond between the
>> two Hydrogen? Any comments? Thanks in advance!
>> Best!
>> Ming

Neelanjana Sengupta, PhD
Physical and Materials Chemistry Division
National Chemical Laboratory
Dr. Homi Bhaba Road
Pune 411008, India
Phone: +91-20-2590 2087

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