[gmx-developers] Constraining massless particles
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Thu Feb 3 21:01:10 CET 2011
As far as I know, there is no way to have sensible dynamics of massless
particles except through virtual sites. A massless particle has infinite
velocity at any finite temperature.
I suspect that you should rephrase the question you are asking such that it
can be answered either using vsite hydrogens, or with noninterating
hydrogens with mass. The shake/lincs equations include inverse masses in
them; you can't get around it.
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Date: Thu, 3 Feb 2011 14:54:02 -0500
> To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>, Discussion
> list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Constraining massless particles
> Well, normally yes. But then I'd have to hack the vsite ilists every
> time I want to turn a particle on or off. I'm trying to avoid that,
> partially because I may not always want to have vsite hydrogens when the
> hydrogens are active. I'm not too picky about exactly where the massless
> particle is positioned, but I figure it may be wise to have it close to
> the heavy atom. The important thing is to have the heavy atom move as if
> the hydrogen wasn't there.
> Shirts, Michael (mrs5pt) skrev 2011-02-03 20.48:
>> 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
>>> 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.
>>> 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/
>>> gmx-developers mailing list
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> 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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