[gmx-users] GRO File Merging

[Sanim Rahman]

Hi all,

I have been using gromacs to design a membrane protein system. I used
CHARMM-GUI to design my membrane and then was able to split my system into
three parts (protein, lipid, solvent) and convert it into .gro format. I am
able to individually view each part in VMD all together but when I use:

*cat protein.gro lipid.gro solvent.gro > system.gro*

The molecule does not show up in VMD. I properly edit the number of atoms
and the box coordinates of the system by using -editconf to correct the box
coordinates. I receive no errors in VMD as well. What should I do to fix
this?

Also when combining topology files, I would convert lipid.top and
solvent.top into .itp files and use the #include statement to combine them
into my protein.top file? After that, my system should be set correct?

Thank You,
Sanim Rahman