[gmx-users] amber99 with berger's lipids
jmsstarlight at gmail.com
Tue Apr 9 09:59:27 CEST 2013
By the way during simulation of the membrane-protein systems in the
Amber99sb ff (with berger lipids) I've noticed decreased of my system in
the Z-direction ( I've observed the same also during simulation of such
systems in the Charm full atomic ff). In both cases the observed effect was
seen in both GPU and non-gpu regimes with different cutoffs.
It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff
with berger lipids) I didnt observe such decreasing in the Z - dimension of
my bilayer. The only difference was in the water models (spc in the gromos
and tip3p in the amber or charm). Might it be relevant ? Should I switch to
the spc water with the amber ?
2013/4/8 Justin Lemkul <jalemkul at vt.edu>
> On Mon, Apr 8, 2013 at 7:50 AM, James Starlight <jmsstarlight at gmail.com
> > In literature I found that the ussage of 1.0 cutoffs should give good
> > results but in the antechamber manual I've seen that usages of 1.2
> > ( with GAFF) should be used. So what cut-offs should I use for
> > protein-ligand complexes done in amber ? (assuming that I simulate my
> > system in the berger lipids )
> Do a few test runs and see. I would think the cutoff value would more
> strongly affect the lipids, not the ligand, whose interactions are
> comparatively few and relatively local. If you use the Verlet cutoff scheme
> in version 4.6, it's largely irrelevant since there will not be any
> "missed" interactions either way.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
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