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

Szilárd Páll pall.szilard at gmail.com
Sun Dec 29 22:26:14 CET 2013

On Sat, Dec 28, 2013 at 1:43 AM, Lutz Maibaum <lutz.maibaum at gmail.com> wrote:
> On Dec 24, 2013, at 2:29 AM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>> Just wondering, has anybody done a comparison with the Verlet scheme?
>> It could be useful to know whether it produces results consistent with
>> the 4.6 group scheme implementation or exhibits different behavior.
> I updated the comparison chart with another simulation that uses the Verlet cutoff scheme:
> http://faculty.washington.edu/maibaum/dppc_comparison/comparison.png
> It might be too early to tell, but I’d say that there is no significant difference between using the Verlet and the group scheme in Gromacs 4.6.5 — they both give an area per lipid that too low (compared to results obtained with Gromacs 4.0.7). Using the Verlet scheme is about two times slower in performance than using the group cutoff scheme.

Note that the Verlet scheme calculated the buffer based on the given
drift, so when using it nstlist can be chosen freely. As it has far
better energy conservation than the group scheme, it may not make much
difference, but you can make the drift (originating from the
non-bondeds) even lower by setting the verlet-buffer-drift mdp option.
I do not expect this to change much though, as what you are observing
is probably caused by something else.


> Best,
>   Lutz
> --
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