Re: water models and some questions

From: David Hardy (
Date: Thu May 07 2009 - 13:54:09 CDT

Hi Jose,

We actually do have support for Drude oscillators in NAMD. We don't
yet document this capability because we are still missing full
support for lone pairs required for the force field being developed
by Roux and MacKerell. The SWM4-DP and SWM4-NDP water models are
fully supported.

The Drude oscillators are integrated using Langevin dynamics
("langevin=on") with a two-temperature thermostat that freezes each
Drude oscillator while keeping its center of mass at room temperature
("langevinTemp=300"). The atomic bonds for water need to be kept
rigid (using Settle). This approach appears to be stable for 1 fs
timesteps. The two new (and undocumented) configuration file options
are "drude=on" and "drudeTemp=1" (or however cold you want the
oscillators, measured in Kelvin). There are enhanced outputs for
energy: DRUDECOM and DRUDEBOND monitor the two temperatures. There
are also DRCOMAVG and DRBONDAVG that average over the previous steps,
analogous to the TEMPAVG averaging for TEMP. You'll see that TEMP
(and TEMPAVG) will be much lower than the langevinTemp since these
measures combine the hot and cold degrees of freedom together.

The PSF needs to be augmented to include the Drude particles and lone
pairs. This includes the NATOM and NBOND sections. There is also a
NUMLP section for lone pairs that is not yet supported by NAMD. The
new interaction parameters can be read in from an additional force
field parameters file.

I don't know about the general availability of structure building
tools and force field parameter files for Drude. Maybe someone else
on this list knows? We don't yet have support in psfgen for building
a Drude PSF.

Best regards,

On May 7, 2009, at 11:57 AM, Peter Freddolino wrote:

> 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,
> Peter
>> Best
>> Jose Antonio

David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois

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