On 23/01/2012 9:27 PM, priya thiyagarajan wrote:
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..
Go and work out how many water molecules at normal density you can have
in a 15nm^3 box.
Mark
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