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

xiaoyi li xiaoyi at xray.bmc.uu.se
Thu Sep 25 17:26:01 CEST 2003

Hi XAvier,

I am a beginner of gromacs. I only read from the manual that there are
position restraints, angle restraints and distance restraints. But i
don't know how to add them in my simulation. Would you like to tell me?

> what kind of constraints do you use. I observed the same as I was using
> h-bond and it disappeared with all-bonds.
> XAvier
> on 9/24/03 4:28 PM, xiaoyi li at xiaoyi at xray.bmc.uu.se wrote:
> > Dear gmx users,
> > 
> > Thanks for Derrick, Anton, Peter and David that I wrote out my top file
> > and gro file and they works at last.
> > 
> > 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?
> > 
> > 
> > Thanks,
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xiaoyi li <xiaoyi at xray.bmc.uu.se>

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