From: Lutz Maibaum (
Date: Tue May 12 2015 - 13:40:07 CDT

On May 12, 2015, at 1:34 AM, Seera Suryanarayana <> wrote:
> Based on above information what I understood is that the .gro file has 35183 atoms including solvent atoms. But in .xtc file has only protein atoms as I have selected protein as output during trjconv execution. Actually I want to load only protein molecule on to vmd after mdrun. Kindly tell me how to overcome this problem.

Starting with your gro file that contains all atoms in the system, you could use trjconv to create another gro file that contains only the protein. You would then have a gro file that has the same number of atoms as your xtc file.

Hope that helps,