you might not have well prepared the topology for the protein

Proteins can't "break" during a simulation. What you're likely seeing is a PBC effect.

http://manual.gromacs.org/current/user-guide/terminology.html#periodic-boundary-conditions

Hi Dr. Justin,

I have applied pbc in all x,y,z,-x,-y,-z directions and saw still looks broken. I have attached the .vmd file below.

Please comment about it.

A VMD state file cannot be loaded without all component files. A screenshot would work fine, but simply *using* PBC in your simulation isn't the issue. Molecules will be "broken" because mdrun does not care about visualization convenience; the physics don't depend on "whole" molecules. They are intact topologically, just visually "split" across the boundaries. The proper "fix" for this is to use trjconv, for which you can find more information in the GROMACS manual.

Hi,

did you check your protein structure in vmd with periodic image? How you decide your protein is broken? first you can check your protein structure to remove pbc.

you can use gromacs tool trjconv with pbc option whole. please follow this link

http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html

Best wishes

you might not have well prepared the topology for the protein

After completion of your production run, use the trjconv command and see if the problem still remains:

gmx trjconv -s .tpr -f .xtc -o noPBC.xtc -pbc mol -ur compact