[gmx-developers] Constraining massless particles
erikm at xray.bmc.uu.se
Thu Feb 3 20:54:02 CET 2011
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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