[gmx-users] lipid kit from Marrink!

Shang-Te Danny Hsu hsu at nmr.chem.uu.nl
Thu May 2 11:27:44 CEST 2002

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!!!

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?


David L. Bostick wrote:

 >I use anisotropic with
 >compressibility         = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
 >It seems to work quite well.  Since the 0.0 compressibilities of the
 >off-diagonal elements keep the box from deforming.

That's the way I do it, but it should definitely be combined with
anisotropic or semiisotropic scaling. In the
liquid crystalline phase it should be perfectly OK to allow cell
deformations too (they won't be large).

 >>There has been some discussions about proper pressure coupling for lipid
 >>bilayer. My experience is that the anisotropic or semiisotropic coupling
 >>with compressibility of 6e-5 or 4.5e-5 along the membrane normal easily
 >>deforms the bilayer in < 20ps and eventually the bilayer is flattened!!
 >>On the other hand, with isotropic or without any P-coupling, the system
 >>is running quite well.

But what kind of surface tension do you get then? The isotropic coupling
will per definition constrain
your system so the membrane cannot thin out or get thicker, but that is
usually not the normal
conditions a biological membrane exists under.

 >>Surface tension coupling method is suggested to be a nice approach (J.
 >>Chem. Phys. 111(3):1281), but the parameters are not trivial. Without
 >>experimental data on hand, it is difficult to estimate surface tension
 >>(in my case, POPC bilayer). In addition, the incorporation of other
 >>molecules may alter the surface tension again!
 >>How should I setup up such a system properly???

Surface tension coupling won't help you; the only reason to do that is
basically to get a non-zero surface tension.
The equilibrium state of biological membranes is the one with lowest
free energy, and unless the cell is pressurized
or something this corresponds to zero surface tension.

I would guess that your topology, parameters or simulation setup has an
error somewhere!

Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl

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