Re: water models and some questions

From: Peter Freddolino (
Date: Thu May 07 2009 - 11:57:51 CDT

Hi Jose, wrote:
> Dear namd developers:
> I am trying to implement different waters models in Namd,therefore I
> have some questions:
> 1. In Namd 2.7b1, what does exactly the command "waterModel tip4" do?

It turns on a section of the code that enforces the constraint on the
position of the TIP4 lone pair, along with making appropriate
corrections to the virial.It also changes how namd integrates the motion
of massless particles(rather than just giving them a mass of 0.001, as
is done in the normal case).

> 2. How Does NAMD recognize the hydrogen atoms? I have the feeling that
> is just a mass criteria, so if I have an atom with mass lower than 1 amu
> is going to be considered as a hydrogen atom? All of this is because I
> want to implement some water models with the drude oscillator model.

Anything with a mass on the open interval (1.0, 3.5) is considered a
hydrogen, anything with a mass on (0.05, 1.0] is a drude, and anything
on [0.0,0.05] is a lone pair -- you can find the relevant classification
in Molecule.C. There is already a drude model currently being adapted
for use in namd; try grepping the code for SWM4. Dave Hardy, who is
working on that code, may have additional comments.


> Best
> Jose Antonio

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