Re: selective rigidbonds

From: Jérôme Hénin (
Date: Fri May 21 2010 - 05:47:29 CDT


It should be fairly easy to do that for water, by defeating NAMD's
mechanisms for detecting water molecules. Basically, NAMD tags
hydrogen and oxygen atoms based on their masses (and names, for
oxygen), then finds water whenever one oxygen is bound to two
hydrogens (all that code is in Molecule.C, if you know a bit of
programming). If you tweak some TIP3P water so that the oxygen atom's
name does not begin with O, I think NAMD will not recognize water.

Applying the same trick to non-water molecules would require
preventing some hydrogens from being detected as such. You could
increase their mass to more than 3.5 amu, or tweak the code in


On 21 May 2010 11:29, Sabyashachi Mishra <> wrote:
> Can I use 'rigidBonds' for 'all' but a few residues and a few water molecules?
> Thanks
> SM

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