hello sir, i like to know few informations regarding box dimension and setting no.of.solvent molecules..
i want to run simulation for different number of protein molecules with same number of water molecules.. i used following commands to increase the no.of molecules i used genbox -nmol 100 -ci protein.pdb -box 15 15 15 -o protein100.pdb then i set box type editconf -f protein100.pdb -bt cubic -o prot100_box.pdb -box 15 15 15 to add water genbox -cp prot100_box.pdb -cs spc216.gro -p topol.top -o prot100_water.pdb -maxsol 50000 when i added 50000 water molecules only half of my box is getting filled by solvent molecules.. i tried 3 times.. i am gettin the same ... can anyone tell me why its happening like this... please help me with your answer.. thanking you,
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