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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