[gmx-users] some peoblems about modeling...

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Mar 23 07:47:23 CET 2009

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.


-- 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!!!

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