Re: exclude 1-2 or 1-4?

From: Peter Freddolino (
Date: Tue May 12 2009 - 10:07:42 CDT

Don't use rigidbonds with CG models... there's no point, as rigidbonds
only affects bonds which involve a hydrogen, and any CG model with
hydrogens running around isn't very CG ;-)

What exclusion form you use depends on the CG model that you use, and
you should check for your specific model, but most of the ones that I'm
familiar with (eg., the Marrink model and its derivatives, martini, and
the shape-based CG model in VMD) use 1-2 exclusions.


doty alexiou wrote:
> Hello.I am running a protein folding simulation in NAMD using CG
> model.I found a message in the mailing list which suggested that
> exclusion should be set exclude 1-2, and not exclude 1-4.However,when
> this was set,was a message : "splitPatch hydrogen is required for
> rigidBonds." We tried with splitPatch hydrogen but we got the same error
> message. Is there any suggestion on that?Thanks.
> ------------------------------------------------------------------------
> Windows Live™: Keep your life in sync. Check it out!
> <>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:47 CST