Re: NAMD and usable FFs

From: Kenno Vanommeslaeghe (
Date: Thu Oct 16 2014 - 13:37:11 CDT

All CHARMM force field releases are technically compatible with NAMD in
the sense that they won't crash. However, what you really need is
confidence that the results of such runs are physically relevant, which
means that you want to be sure the different force field files you read
into psfgen and NAMD are compatible with one another. While the CHARMM
force field's nonbonded "foundations" and parametrization philosophy
haven't changed much, issues related to atom typing *might* occur when
mixing parts of CHARMM that were not meant to be used together. In this
respect, the pre-36 situation was somewhat confusing, in a large part due
to the existence of unfortunately named combined files. Apart from the
important improvements in the physics (as discussed in the CHARMM36
papers), one of the big goals of CHARMM36 was to clear this up this
confusion. For these reasons, the pre-36 force fields should be regarded
as as obsolete. So in summary, I would strongly urge you to download
CHARMM36 from the Mackerell lab website and use CHARMM36 for all parts of
your system.
Doing so not only gives you a modern force field that correctly handles
the phenomena at the simulation time scales that are currently becoming
accessible, but also frees you from any compatibility worries. Here are
more concrete instructions (if you're not using CGenFF, just ignore the
molecule.str part):

On 10/15/2014 05:34 AM, Francesco Pietra wrote:
> Hello:
> It is not clear to the general - mostly experimental - user, which CHARMM
> FFs for proteins, metalloproteins, and organic ligands are compatible with
> NAMD 2.10.
> For example, with namd2.10 I currently use toppar_all22_prot_heme.str for
> dioxygen in combination with top_all27 and par_all27 for the protein.
> Could I use a more recent version of CHARMM FF with that toppar? This is
> just an example, a general table of compatibility would be most welcome,
> especially in view of using CGenFF.
> thanks
> francesco pietra

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