I want to ask about energy minimization. I want to create DGDG lipid bilayer, which is consist of 128 DGDG molecules (64 per layer). So I created a molecule in Pymol. Should I try to do energy minimization:
a) after I create a single molecule to get properly conformation and again after I create lipid bilayer do energy minimization (energy minimization whole bilayer); (2 energy minimization)
b) only after I create lipid bilayer; (1 energy minimization).
I ask about this energy minimization, because DGDG 3D structure is too flexible and there is no information in the Internet about their structure and I am not sure that after I create these glycolipids in bilayer they will have properly conformation after energy minimization.
You can always try a shorter approach by just building up the bilayer from non-minimized molecules and see if it works. I would definitely give it a try.
If it doesn't work then this should be a safe although quite laburious way:
1) Take your single molecule, minimize it in vacuum.
2) Build the bilayer out of the minimized molecules but make them enough space not to overlap. The bilayer will at first have higher area per lipid then expected at the end.
3) Add solvent and minimize this large bilayer.
4) Apply lateral pressure in xy plane to squeeze the bilayer. This can be done by 1000 bars at low temperature (like 50K for example).
5) Let it heat under slow thermostat.
6) Equilibrate the resulting structure at your target temperature for some tens of nanoseconds.
I think its better when you create bilayer then you can do minimization and short equilibration. Then you insert protein in to bilayer following gromacs tutorial.
http://www.mdtutorials.com/gmx/
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