[gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5
lutz.maibaum at gmail.com
Wed Dec 18 19:24:58 CET 2013
On Dec 18, 2013, at 8:50 AM, Sabine Reisser <sabine.reisser at kit.edu> wrote:
> Up to Gromacs 4.0.7, the long rance forces, which are calculated at every nstlist'th step, were added constantly to the short range force in the subsequent steps. Starting from Gromacs 4.5., the long range force is added nstlist times to the short range force on the nstlist'th step, while there is nothing added to the short range force on the subsequent steps. This creates some kind of impulse force which we believe is responsible for the different behaviour of the membrane, although we haven't figured out the exact mechanism yet.
That's interesting. Now I see that this change is documented in the manual (Section 3.4.7). Would that imply that this effect does not depend on the model for long-range electrostatics (Reaction Field or PME), but it comes from using twin range cutoffs?
> I expect you to get the 'right' area per lipid if you use nstlist 1 as already suggested by Mirco, because in that case the multistep algorithms give the same answer. This is also our experience with G54A7.
I started a run yesterday with nstlist=1, and so far (about 12 ns) the area per lipid indeed stays at the "correct" value of around 0.63 nm^2.
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