I have a problem. I have this warning when I minimized my DGDG membrane.
NOTE 1 [file step6.1_equilibration.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
NOTE 2 [file topol.top, line 24]:
System has non-zero total charge: -0.038408
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
WARNING 1 [file topol.top, line 24]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
Note 1 is it big problem? I think about changing
tcoupl = berendsen → tcoupl = v-rescale
Note 2
I have nothing in line 24 in my topology file (my topology file has only 23 lines). It’s only -0.038408, so maybe I shouldn’t add any ions.
Warning 1
I dont know what I should do. I use -maxwarn 1 option. Counter ions? My system has only -0.038408 charge
I created my DGDG (128 lipids 3840 water molecules, OPLS-AA force field) membrane in that way:
1. I created DGDG molecule in pymol
2. I rotated them to have acyl chains along Z axis: gmx editconf -f DGDG.pdb -o DGDG_rot.gro -rotate 0 0 90 -box 1 1 1.1
3. I created layer and rotated each lipid by random angle: gmx genconf -f DGDG_box.gro -o DGDG_down-layer.gro -rot -nbox 8 8 1 -renumber -maxrot 0 0 360
4. I created up-layer: gmx editconf -f DGDG_down-layer.gro -o DGDG_up-layer.gro -rotate 180 0 0
5. I translated up layer: gmx editconf -f DGDG_up-layer.gro -o DGDG_up-layer_trans.gro -translate 0 8 -1.1
6. I fused two layers into bilayer: cat DGDG_down-layer.gro DGDG_up-layer_trans.gro >> DGDG_membrane.gro
7. I added water: gmx solvate -cs -o water_slab.gro -box 8 8 1.3
gmx editconf -f water_slab.gro -o water_slab-up.gro -translate 0 0 2.02
gmx editconf -f water_slab.gro -o water_slab-down.gro -translate 0 0 -4.35
8. Final system assembled: DGDG_membrane.gro water_slab-up.gro water_slab-down.gro > membrane.gro
9. I created topolgy by using LigParGen http://zarbi.chem.yale.edu/ligpargen/
10. In the past 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.
11. I equilibrated and used in equilibration mdp file from Charm-gui membrane generator
12. I run the simulation and used in dynamics simulation mdp file from Charm-gui membrane generator
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