[gmx-users] regarding box dimension and number of solvent molecules

priya thiyagarajan priya.thiyagarajan09 at gmail.com
Mon Jan 23 11:27:55 CET 2012

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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