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I am working on the CG Simulations with large
systems. During PBC definition I used gmx edifconf -f -bt cubic
-d 1.0 -o tried this and also increased the box size 60 60 60. Then
during ionisation, it showed an error which I have attached with the
mail. I tried to solve this error by increasing the box size 80 80 80
also still the same error message. Since I removed some water
molecules after solvation do you think error because of that? In my
mdp file list value is about 1.0. Kindly please help me. I look
forward to hearing from you.
Error : The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease the rlist
A box size of 60 60 60 should definitely be enough. Could you post the full command line you used when getting that error? Could you post the last line of the .gro file you are using? What are your rvdw and rcoul values in your .mdp file?
cmd used in grompp :
gmx grompp -f -c -p -o .tpr and the last line of the gro file was 0.00 0.00 0.00 and rvdw 1.2 I think gro file last line was the error. I found the issue was solved. Thankyou