Your question does not make much sense to me. Can you please explain in greater detail what you're trying to do?

I want to study the structure changes of two similar proteins in presence of two or four heme. The protein about 42 aa and I am doing 50ns simulation. I want to know how to add the heme to simulation. Can anyone suggest on this topic? I am using the following paper for this simulation. I just want to know how to add heme to simulation

The Gromacs program genbox can insert molecules with the -ci -nmol options.

I am using the following gromacs program genbox but not understanding the -ci - nmol file how to add this heme molecules please the explain of this file.

The -ci flag specifies the coordinate file of the molecule to insert. The -nmol flag is how many molecules to insert in the box.

Thank you

Justin: I have .gro and .top file for single molecule (lets say ethane). I want to create larger 'polymeric' sample so I reproduce the molecule nmol-times in larger box by genbox command. But how to force program to write down the new topology file for this bigger system? Option like -p new.top did not work for me (file input/output error). The whole command is:

genbox -ci conf.gro -nmol 300 -box 3 3 3 -o box.gro -p new.top

genbox will never automatically update the topology for anything other than water; the residue name is hard-coded.  You have to do the update yourself in a text editor.

Thanks! That makes things more difficult for preparing the input. Is it better to modify .top file or .pdb file (I created one for my own)?