[gmx-users] Difference in omega angles!!

Seera Suryanarayana palusoori at gmail.com
Sun Aug 13 22:30:09 CEST 2017

Dear gromacs users

First I have done simulations of peptide for 100ns. And then I have
generated the .pdb file after energy minimization by following commands

gmx trjconv -s em.tpr -f em.trr -o em.pdb

After generation of PDB file, I did mutation at one position in em.pdb file
and named it em_mt.pdb. Then generated topology file, created box, solvated
and added the counter ions to em_mt.pdb's simulation system to neutralize
the system. After this I have done energy minimization with complete
protein restrained. As I restrained the peptide during energy minimization,
I expected the same torsion and omega angles in em_mt.pdb after energy
minimization. But I got some different omega angles  when I compared with
the omega angles of em.pdb. The maximum difference is 5. what could be the
reason in difference of omega angles between em.pdb and em_mt.pdb, even
though the later one is restrained?

Thanks in advance
Graduate student

More information about the gromacs.org_gmx-users mailing list