[gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

Sabine Reisser sabine.reisser at kit.edu
Wed Dec 18 17:50:34 CET 2013


I ran into the same problem comparing the subsequent G54A7 lipid force 
field for DPPC.
We could trace the relevant (trajectory-changing) differences in the 
code down to the transition Gromacs 4.0.7 -> 4.5., and here to the 
change in the multistep update algorithm.
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.
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.


On 12/17/2013 11:45 PM, Mirco Wahab wrote:
> On 17.12.2013 20:58, Lutz Maibaum wrote:
>> What would the next step be trying to debug this issue?
> You could, just for debugging, give nstlist=1 a try
> (instead of nstlist=5)?
> I tried this today on a "quadrupled" version of your
> system (duplicated in x, and y direction, 512 lipids),
> which resulted at an area of around 0.605 nm² (still
> growing, incredible slow computation). The very same
> system at nstlist=5 ends up at around 0.575 nm².
> Maybe this is a hint for the developers?
> Regards
> M.

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