Re: S-S bond

From: Giacomo Fiorin (
Date: Sun Feb 20 2022 - 18:35:50 CST

Hi Paul, you can manually add an empirical bond via extraBonds:
Although you can't do it during a simulation, you can certainly read binary
restart files, turn on the new bond, and continue from there. What isn't
obvious at all is how to deal with the hydrogen atoms, or to update the
charges and vdW coefficients of the atoms involved in the reaction to
reflect the changing chemical environment. One is probably better off
switching between topologies, as is done for example in the NAMD
implementation of constant pH simulations.

If one wanted a *continuous* description of the chemical reaction, then it
wouldn't be just a matter of changing the source code, but rather defining
a suitable force field to describe the reaction. Biomolecular force fields
like CHARMM or AMBER are not designed to simulate reactions. Of those that
do, I don't think there are any that provide the same combination of low
computational cost and decent accuracy of the intermolecular forces that
are most important in biophysics. Even DFT (i.e. including the electrons
to a certain degree) kind of stinks at describing intermolecular forces,
unless you use a very modern functional that is also more expensive and
difficult to use in a transferable manner.

So basically, if one accepts that there isn't a good enough simulation
model to describe the thermodynamic cost of a continuous reaction,
simulating the two endpoints separately (with and without the disulfide
bridge) with standard force fields is what is usually done.


On Sun, Feb 20, 2022 at 9:08 AM Dalhaimer, Paul Matthew <>

> All,
> Has anyone tried to modify the NAMD source code to allow for covalent bond
> formation during a simulation? Cysteine-cysteine, would be an obvious
> target to try this on.
> -Paul

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