[gmx-users] protein has broken after 100ns simulation

[Seera Suryanarayana]

Dear gromacs users,

I have simulated protein for 100ns. When I visualized the protein in VMD, I
have seen the protein into different fragments. Later I came to know that
there is no breaking phenomena in simulations and that is because of the
PBC problems. I have executed the trjconv command with following arguments
to solve the problem, but I couldn't make it successful. I also attached
the snapshot. Kindly guide me how to resolve problem?

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -center -pbc
mol -ur compact

Surya
Graduate student
India.