From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Oct 30 2008 - 08:02:52 CDT
Your interpretation is correct. To the best of my knowledge NAMD 2.5
behaved in the same way but just didn't print a warning to explain it
(since the net result should be the same).
Neelanjana Sengupta wrote:
> 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 incorrect.
> On Wed, Oct 29, 2008 at 9:37 PM, Peter Freddolino
> <petefred_at_ks.uiuc.edu <mailto:petefred_at_ks.uiuc.edu>> wrote:
> Purushottam Dixit wrote:
> 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.
> On Wed, Oct 29, 2008 at 11:20 AM, Ming
> <mailto:ebullience_at_emails.bjut.edu.cn>>> wrote:
> Dear all,
> I am trying to simulate my system using namd with the
> 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!
> 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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