[gmx-users] genbox

Dinesh Pinisetty dpinis1 at lsu.edu
Fri Aug 13 18:09:49 CEST 2004

Respected users,
         I have two questions they might look silly but as i am a beginner
it is very important for me to know answers to them...
1)I have taken a molecule of DPPC and created a
bilayer on my own using genconf and editconf
commands.Now before doing Energy minimization I want
to add water and then perform energy minimization.If I
am using genbox command to add water molecules it adds
64,245 molecules which is very very high number,I want
to add 60 per molecule of DPPC I have 96 DPPC
molecules,i.e I want to add 96*60 5760 molecules,how
to have control on adding water molecules in the box.I
heard from Dr.ANTON FEESTRA that genbox adds water molecules basing on box
size my box size is just above half the cut-off which is a requirement i.e.
even my box size is not so large(I used -d 0.75 in editconf).
       In the pdb file of Dr.Tielmann's site water molecules are present
did they add them using genbox if so how could they control the number?

2) My second question is if I also want to add sugars
etc in the system,can I do that using the pdb file I
have downloaded from Dr.Tielmann's site.I mean how to control the x,y,z
co-ordinates while adding. The pdb file in Dr.Tielman's site when
visualized water is outside of the membrane on both sides similarly I want
to add sugars
on both sides along with water but how to see that
co-ordinates of the sugar atoms make them to settle
along with water outside the bilayer.

Please let me know answers for the above questions,I would be grateful to
you if you could answer me the above
Thanking you,
Dinesh Pinisetty.

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