Re: Molecular Dynamics of Rigid Linear Molecules in NAMD.

From: Axel Kohlmeyer (
Date: Sun Sep 28 2014 - 13:31:59 CDT

On Sun, Sep 28, 2014 at 2:06 PM, Kenno Vanommeslaeghe
<> wrote:
> No. Large harmonic restraints (i.e. large enough to mostly prevent a bond
> from stretching) would cause *exactly* the same integration time step issue
> as large bond force constants; to the integrator, there's no difference. We
> just had this whole discussion less than a month ago;
> The NAMD developers didn't react that time, and neither did they on an
> earlier closely related thread, so I'm henceforward going to assume it is
> not possible to define rigidBonds between heavy atoms, meaning you'll have
> to use a different simulation software. If so, dear NAMD developers, I
> myself have absolutely nothing to gain from it, but there does seem to exist
> a certain demand for rigidBonds between heavy atoms...

FYI, for a linear molecule like CO2, this is not enough. you also need
to constrain the angle, and that is a very tricky issue, since at 180
degrees, the usual SHAKE algorithm leads to degenerate solutions.

there are two straightforward alternatives: 1) use a rigid body
integrator (also needs a short(er) time step) 2) recast the 3 atomic
linear molecule into to a diatomic for the purpose of time integration
using two dummy atoms. then you can use SHAKE (and RATTLE) and a
fairly large time step. solution 1) is for example implemented in the
LAMMPS, solution 2) in GROMACS.

the topic of having a chain of connected rigid bonds as used by the
TRAPPE force field comes up every once in a while on different mailing
list, but what most of the people asking about this don't realize is
that a) the force field is developed by a group that focuses on MC
simulations (where rigid bonds and constraints are a non-issue) and
that b) doing such a thing in a parallel(!) MD code is pretty
non-trivial as the constraints equations could affect atoms in
multiple domains (or patches in NAMD-speak), which would require
communication at every iteration step. i cannot speak for the NAMD
developers, but in the LAMMPS community people have decided to wait
for a user that wants this feature so much that he/she would sit down
and implement this feature. unfortunately, as soon as people realize
*how* difficult this is, they (so far) have all given up.


> On 09/28/2014 07:50 AM, Mike Makowski wrote:
>> Javad,
>> Harmonic restraints are your best bet. You'll have to include parameters
>> in
>> your CHARMM FF parameter file and also in your NAMD config file. See this
>> CHARMM documentation:
>> They explain how to keep a residue rigid.
>> Mike
>> Michael Makowski
>> University of California, Irvine
>> Department of Chemistry,
>> Chemical and Material Physics,
>> Irvine, CA 92617
>> Cell: 267 588 9865
>> Office: 949 824 5776
>> On Sun, Sep 28, 2014 at 4:02 AM, Javad Noroozi <>
>> wrote:
>>> Mike,
>>> First, what you mean by incorrect assumptions?
>>> TraPPE and CHARMM use the same functional form for non-bonded and some
>>> bonded(bonds and bending) potentials. So,one can convert the parameters
>>> between the two force fields.The problem is that TraPPE use rigid bonds
>>> which is equivalent to very large spring constant in harmonic potentials.
>>> I
>>> want to know if there is any way to handle the rigid bonds in NAMD
>>> similar
>>> to virtual sites used in Gromacs tutorial?
>>> To my knowledge,the SHAKE algorithm implemented in NAMD works for water
>>> molecules only.
>>> Bests,
>>> _____________________
>>> Javad Noroozi,Department of Chemical Engineering,Sharif University of
>>> Technology
>>> Email:
>>> ________________________________
>>> From: ‪Mike Makowski‬ ‪<>‬
>>> To: ‪Javad Noroozi‬ ‪<>‬
>>> Cc: ‪""‬ ‪<>‬
>>> Sent: Sunday, 28 September 2014, 11:33:10
>>> Subject: Re: namd-l: Molecular Dynamics of Rigid Linear Molecules in NAMD

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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