[gmx-users] amber99 with berger's lipids

Christopher Neale chris.neale at mail.utoronto.ca
Tue Apr 9 21:05:55 CEST 2013

Did you correctly account for the different 1-4 scaling factors in the Berger and Amber lipids (either by obtaining .itp files from the authors of the Berger lipids-Amber protein article or making the changes yourself)? If not, then you are doing your simulation incorrectly (see their paper for why).


-- original message --

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 ?


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