From: Aron Broom (
Date: Mon Jul 14 2014 - 13:18:14 CDT

There is not an NAMD forcefield. NAMD can use CHARMM, AMBER and other
forcefields, so the angles and such for hydrogens would be related to those

Restraint algorithms like SHAKE can be employed, but they don't need to be.

If you add a hydrogen to make an acid sidechain neutral, or remove one to
make a base neutral, you need to also remake your parameter/topology file
to reflect that. What options you have for neutral side-chains will depend
on the forcefield. In AMBER for instance, I think neutral options for Asp,
Glu, His, and Lys, have been parameterized and added in by the AMBER
forcefield developers, but not for Arg.

Regardless of the program that chooses the hydrogen's positions, they
should be extremely close to the same, and any differences would be gone
within a very short simulation time.

On Mon, Jul 14, 2014 at 2:05 PM, Eifler, Jay Q. (UMKC-Student) <> wrote:

> I cannot find a reference on how NAMD adds its hydrogens.
> Chimera fully explains for example.
> I also am wondering if I use another program to add hydrogens
> but then minimize my structure in NAMD doesn't that
> just readjust the hydrogens to NAMD's force field parameters?
> So then shouldn't we just use NAMD's add hydrogens facility
> rather than other methods to be consistent? I've noticed that
> neutral protonations just adjust back to the odd looking structure
> with a hydrogen apparently deleted.
> Maybe I have some confusion about the hydrogens. Also,
> I thought they were held rigid with SHAKE or something.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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