[gmx-users] loiuc vermeer-seperating bilayers.

Eric Jakobsson jake at ncsa.uiuc.edu
Sat Sep 10 20:40:23 CEST 2005

If you are doing everything really right, you can melt a bilayer from the 
dehydrated crystal structure and get a stable bilayer.  That was what we 
did very early ('95) to be sure that we were not simply finding the answer 
that we has assumed from the start, thereby burying whatever methodological 
mistakes we were making.

At 11:34 AM 9/9/2005, you wrote:
>Dear Louic,
>I had this problem a couple of weeks ago and when i posted the questions erik
>kindly replied back. However, the one thing that did work for me was that 
>i ran
>an NPT simulation with an increased tau_p. Earlier i was using a tau_p of 0.5,
>but when i increased it to 5.0, the seperation dissappeared, albeit
>  Also one thing that i think helps is to run the simulation intially with NVT
>ensemble and then switch to NPT with the above mentioned parameters. 
>However, i
>m beginning to understand the importance of properly equilibriating a bilayer
>for long times before using it for actually running it.
>I dont know if it helps, but let me know.
>The important thing is not to stop questioning. Curiosity has its own 
>reason for existing...
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

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