[gmx-users] Re: Setting up a complex membrane simulation

jonas87 jonas_dehairs at hotmail.com
Mon Nov 12 13:03:51 CET 2012

Ok, what i've currently done:

I start with a pdb file of a single molecule Lipid_A and its topology and
put it in a box:

editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0

I want a total of 128 molecules of this lipid in my system so I use genbox
to add 127 more:

genbox -cp Lipid_A-box.gro -ci Lipid_A.pdb -p Lipid_A.top -o 128_Lipid_A.pdb
-nmol 127

This only ads 8 molecules, I'm going to guess because more don't fit in my
box. How do I deal with this? How can i know in advance how big i have to
make the box?

kind regards,

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