I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotate 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/ I dont know why my layers seperate and water go into the center of box after minimization and also my minimization have only 130 steps.
membrane_box.gro – before minimization
em.gro – my lipid bilayer after energy minimization
also I put some image how it looks
topol.top2 -topology
Hello
I think in your system there is some free space thats why after minimization your system looks like this which you mansion. You can use CHARMM-GUI to make an initial lipid bilayer structure and you can follow GROMACS tutorial how to build initial input file and doing minimization. http://www.mdtutorials.com/gmx/membrane_protein/index.html
Best wishes
There are several problems that should be rectified. The first is not so much a "problem" as it is a visualization inconvenience. Your system is not centered within the defined periodic box. Hence, the output you get is "split" across periodic boundaries. See the attached screenshot of your starting coordinates. You can use editconf to center the coordinates appropriately.
The bigger problem is the massive amount of void space in the system and the lack of water. During equilibration, the water is likely to soak into the lipids and impede equilibration. Moreover, due to the spacing of the lipids, the waters are very thinly spread out, meaning your lipids are probably going to "see" each other across periodic boundaries, leading to artificial forces that again will impede equilibration.
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