[gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5
patrick.fuchs at univ-paris-diderot.fr
Tue Dec 17 08:04:59 CET 2013
Le 16/12/2013 23:47, Mirco Wahab a écrit :
> On 16.12.2013 21:10, Lutz Maibaum wrote:
>> I am running MD simulations of DPPC bilayers with the Gromos force
>> field, and I am seeing some differences between using Gromacs 4.0.7
>> and 4.5.5/4.6.5 that I do not understand. It would be great if someone
>> had any insight into what's going on here.
> Lutz, from your provided files I can read you use
> twin-range cutoff RF-electrostatics for 54A7:
> rcoulomb = rvdw = 1.4 at rlist = 0.8 w/nstlist = 5
These are standard values with GROMOS force field (together with
reaction field), and they were used by the original authors of those
DPPC lipids. I suspect more an issue with RF implementation in versions
>= 4.5.* since, as Samuli said, with PME there's no significant
difference between 4.0.7 and 4.5.3.
> are these values intended? I remember a posting of Berk Hess
> some time ago where he mentioned that the "newer" Gromacs
> versions would get a better intergation scheme for this
> case (I could not find the source). This might be one of
> the reasons for such discrepancies?
> BTW - a good check would be a simple box of say 15,625
> SPC water - at which water density would the combination
> of your parameters and the actual algorithm knock in.
Dynamique des membranes et trafic intracellulaire
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