[gmx-developers] Constraining massless particles

Erik Marklund erikm at xray.bmc.uu.se
Thu Feb 3 20:44:42 CET 2011


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/

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