[gmx-users] lipid kit from Marrink!

[Erik Lindahl]

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 :-)


Cheers,

Erik