I have a question. I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotated this molecule to have my acyl chain along z-axis. Then I created 8x8 down layer and rotated each lipid along z-axis I also created up-layer. I fused both layers into bilayer and put water in both side of membrane. I built topology by using LigParGen (I use OPLS-AA force field) http://zarbi.chem.yale.edu/ligpargen/. Then I minimized energy.

Now I have a problem. Which equilibration .mdp file I should use?

A) I used charmm-gui (http://www.charmm-gui.org/) to build DOPC bilayer (this is my reference membrane, DGDG is absent in charmm-gui), so I used step6.1-6.6_equilibration.mdp to equilibrated my DGDG membrane.

B) Also I see that in this tutorial http://www.mdtutorials.com/gmx/membrane_protein/06_equil.html there are two equilibration file:

a) for NVT equilibration

b) for NPT equilibration

So which equilibration .mdp file should I use A or B or maybe something else?