On Tue, Feb 21, 2017, Chris Neale wrote:
> Or generate the charmm topology in gromacs (expanded topology file via gmx
> gromp -pp option) and run that through the parmed tool gromber. That's what
> I do, but only because I am more familiar with gromacs than with charmm or
> namd.
>
> For that usage, single point energy evaluations between gromacs and amber
> (both using charmm36 protein and lipid) are close but not exact. Though
> note you need in this case to rename your water atoms or set the pmemd
> inputs so that it knows how to settle the water properly.
It would be good to get details of your example. We have critically tested
chamber conversions to ensure real reproducibility of the CHARMM force field.
I've heard reports that gromacs and amber are handling improper torsions
in different ways, but have no experience with gromacs myself. Of course, the
differences you are seeing might arise for some completely different reason.
Also, sounds like gromber should be (trying to) get the water nomenclature
change done, if possible....it's too easy for someone to forget to add the
renaming commands in the sander or pmemd input files.
cc-ing to the Amber developers' list, in case someone wants to volunteer
to track this down--it's really rather important that force fields give
consistent results on different platforms.
....dac
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Received on Thu Feb 23 2017 - 05:30:05 PST
