[gmx-users] lipid kit from Marrink!
lindahl at stanford.edu
Thu May 2 19:01:57 CEST 2002
Shang-Te Danny Hsu wrote:
> Dear Erik,
> Thank you very much for your comment!
> TO be honest, I am using a "tool kit" from Siewert Marrink in which
> the topology and parameters of POPC were already defined and a
> pre-equilibriated 64-POPC/water box was also there. I suppose this is
> one of the protocols that you and Marrink published in JACS, 123:8638
> regarding the spontaneous aggregation of bilayers. However, It could
> be the problem of GMX version update from 2.0 to 3.1 and thus some
> experimental settings or statements were different. I try to rerun a
> test simulation with a very short time (100ps) with the anisotropic
> coupling protocol defined in Marrink's mdp file. The system collapsed
> as I just described. That's why I am looking to a solution to this!!!
All the simulations in that paper were run with a prerelease version of
3.0, and my group in Stockholm are using 3.1 for membrane simulations
with good results, so I can't imagine it's the program version.
> In addition, I am simulating a undecaprenyl lipid tail in the membrane
> and micelle systems. I understand that the reason the switch on the
> Ryckaert-Bellemans parameters for the lipid tail is to improve the
> relaxation properties of the long stretch of the tail, which will be
> also important for the unsaturated undecaprenyl tail as well. Would
> that be tricky for the implementation of such a system?
In general, R-B or Kuwajima dihedrals are better for long united-atom
hydrocarbon chains, but it won't crash your system if you use normal
dihedrals & 1,4-interactions instead. (If you use normal dihedrals
without 1,4 interactions it might crash, though :-)
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