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, -- View this message in context: http://gromacs.5086.n6.nabble.com/Setting-up-a-complex-membrane-simulation-tp5002607p5002885.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
