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i am doing the md simulation of pure /mix membrane of phospholipids and glycolipids , i have attached the pbc box file its okay but when i am doing the energy minimization step my structure is broken how to fix this solution. i have attached both gmx gromp and minimization output
Is the box size correctly set? Can you visualize the box boundaries in your pre-minimization structure?
yes sir the box is correctly set i used the commands
gmx editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 9.50000 8.00000 8.00000 .Can u please tell me what does means of
Can you visualize the box boundaries in your pre-minimization structure?