AMBER Archive (2002)

Subject: Re: Is H-bonding really there?

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Sep 27 2002 - 17:04:37 CDT

Hi Suvendu,

I am not sure if I understand your question because I do not see exactly
what is the relation you think it exists between velocities assigned to
the atoms in your system and the presence of hydrogen bonding.

In most MD simulations atoms are considered as being harmonic oscillators.
According to the zero-point energy concept, the energy of the ground state
is not zero as the lowest classical energy is but h*niu/2. So your
atoms will/should never sit still :) (h is Planck's constant and
niu is the frequency of your oscillator)

There is a good book where you can read more about these things:
"Physical chemistry, a molecular approach" by Donald McQuarrie and J. D.
Simon.

Let me know what exactly you thought by relating velocities with
H-bonding.

Additional question: how do you initialize the velocities?

Regards,
Ioana

On Fri, 27 Sep 2002, 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.
>
> __________________________________________________
> Do you Yahoo!?
> New DSL Internet Access from SBC & Yahoo!
> http://sbc.yahoo.com
>
>