Re: Is H-bonding really there?

From: Pratul Agarwal <>
Date: Fri 27 Sep 2002 13:58:25 -0700 (PDT)

You seem to be mixing issues here, it is not clear to me where you
think the paradox is regarding the Hydrogen bonds.

Kinetic energy (and therefore velocities) are related to Temperature by
 <KE> = Sum of 1/2*m*(vel.)^2 = 3/2*N*kb*T

KE = kinetic energy, N= nos. of partciles
kb = boltzmann's constant, T = temperature (in kelvins)

So even when water is in solid phase (ice) the atoms do have velocities
microscopically. You may not "see" the water molecules move but the
thermal motions are present even in ice.

--- suvendu lomash <> wrote:
> HI !!
> I 've been equilibriating water in a solvated box
> using the gradual warming approach. I don't have any
> problems as such - just a thought here. I get the
> impression from MD output files that AMBER can
> simulate H-bonding. If this is true, then during my
> gradual warming of the solvated box I should not get
> any velocity of water molecules till I cross the
> temprature of 273K because they should be in a rigid
> 3d cage structure (ice). why is there this apparent
> paradox?
> thanks.
> Suvendu.
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Received on Fri Sep 27 2002 - 13:58:25 PDT
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