[gmx-developers] Constraining massless particles

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Thu Feb 3 20:48:35 CET 2011

Isn't this what dummies are for?  If they have no mass, there are no
"correct" dynamics for them via integration of the equations of motion; the
only way for them to move in a physical way is through rigid body motions
with attached mass-full atoms, via the dummy atom functionality.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 3 Feb 2011 14:44:42 -0500
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: [gmx-developers] Constraining massless particles
> Hi,
> For the development that I do I sometimes need massless non-interacting
> hydrogens that are bonded to heavy atoms. How can I constrain those
> bonds? If I set invmass=0 for them, then both lincs and shake seem to
> work incorrectly since the heavy atom would move, but not the inert
> hydrogen. I can reposition the inert hydrogens by other means after the
> constraint step. However, if you could think of a smart way of having
> lincs (and possibly shake) move the atoms as if the hydrogen were indeed
> massless I'd be thrilled to hear it.
> Ideas so far are to either:
> * Setting r to zero for all constraints involving massless particles.
> * For massless particles, don't move the heavy atom, just put the
> massless particle at the reference distance and don't move the heavy atom.
> Would those approaches work or would they screw things up in ways I
> haven't thought about? Alternatively, I could remove the relevant
> constraints from the ilist whenever I make a particle massless, but then
> I'd have to reposition the massless particle later.
> Cheers,
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
> -- 
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