[gmx-users] Re: how to constrain the position of DPPC and water

[Dallas Warren]

>My system is DPPC bilayer with water outside and two coumaryl molecules
>in the middle. However, after run the MD, I find some DPPC molecules run
>out of the bilayer and mixed with water. The high ordered arrangement of
>DPPC bilayer has changed too much. But I want the DPPC and water to be
>the environment and relatively fixed, and only coumaryls in the middle
>can move freely. I will be appreciate if someone tell me how to achieve
>this?

That sounds rather unusual.  What time frame of the simulation is this?

Unless something is wrong with the confirmation or the simulation, even in 
a 100 ns simulation it is very unlikely to see a lipid molecule actually 
leave the bilayer.

Are you using anisotropic pressure coupling to allow the box to deform with 
the bilayer as it relaxes to its stable state?

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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