When I solvated a protein complex with about 40,000 atoms, the CHARMM program crashed giving a hint:COUNTER VARIABLE HAS EXCEEDED ITS MAXIMUM ALLOWABLE VALUE. Only one variable displayed, NODON, has exceeded its maximum value MAXPAD=72000. I searched the forum, but couldn't get a clear fix method. So I try to modify the MAXPAD=140,000 in the dimens.fcm file and recompile it, and fixed the problem temporaly. Is it advisable to do so?
btw: I compiled CHARMM with huge version, so it is imposible to move up the size...
Any suggestion is appreciated.