Please don't double post. We saw the first one.
1. That is a question with a lot of options. Do you want a grid of proteins? then try genbox -cp empty_big.gro -cs one_protein.gro
2. What do you mean by remove pbc? Try trjconv -pbc mol -ur compact to get an "enforced" pbc, or starting from a "desired" pbc at the t=0 timestep then trjconv -pbc nojump -s that.tpr
3. I do lots of lipid-protein simulations and yet I have no idea what you mead by adding nanostructure to the lipid bilayer.
In general, you should: a) not double post b) try to put one question per post c) explain your problem / quest a lot better. Chris. -- original message -- Hi, All!! I have four questions: (1) How can I add more than one protein into a cell with PBC, maybe 10 proteins? How can I modify the command of editconf and genbox to achieve the above function? (2) How to remove the PBC of the cell? I use the option '-pbc no' in the editconf fiat, but it can not be recognized by GMX? (3) If I want to add some nanostructure into the lipid bilayer structure, how can I modify the position of the added molecules in the cell? Thanks a lot!!! _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
