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?
The tutorial files using settings for the GROMOS force field. Do not use them for a CHARMM system.
There are many different approaches for equilibrating any molecular system. There is no one "right" way to do it. The CHARMM-GUI approach is very robust for membranes so you can use it directly.
I suggest you to use verified force fields (FF) parameters for DGDG. I have no experience whether LigParGen generates appropriate topology with correct FF parameters. However, you can find martini coarse grained parameter for this lipid: http://www.cgmartini.nl/index.php/force-field-parameters/lipids2/351-lipid.html?dir=Glycoglycerolipids&lipid=DPGG .
In addition, the packmol package is quite suitable to create bilayers.
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