[gmx-users] regarding box dimension and number of solvent molecules
priya.thiyagarajan09 at gmail.com
Mon Jan 23 11:27:55 CET 2012
i like to know few informations regarding box dimension and setting
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..
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