[gmx-users] Regarding minimization of POPE:POPG lipid bilayer

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Jun 24 19:47:49 CEST 2007

>   I built a POPE:POPG bilayer in 3:1 ratio.

Simplify. Start with pure POPE and pure POPG first.

> When I am minimizing the  bilayer, bonds in head groups are breaking
> in POPE and POPG lipid  molecules.

Your topologies are incorrect. Start with a simple test system: a
single POPE in vaccuum.

> while creating *.tpr file using the above file for minimization, I  
> am getting fallowing message.............
>   calling /lib/cpp...
>   In file included from pg-pe.top:5:
>   dpopg.itp:10:8: warning: multi-line string literals are deprecated

Why not take a look at line 10 (or line 8) in dpopg.itp?

You are still a long way from simulating a protein in the bilayer. May
I recommend that you try a little harder to solve your problems before
posting (e.g. by reading the warning messages carefully and seeing
what they mean for yourself, or by trying to find a simpler test
system to narrow down the problem). In this way you will avoid  
decreasing your likelihood of receiving answers to the harder problems  
you may encounter.

Good luck.

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