[gmx-users] Difference in omega angles!!

Justin Lemkul jalemkul at vt.edu
Sun Aug 13 22:31:29 CEST 2017

On 8/13/17 4:30 PM, Seera Suryanarayana wrote:
> 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
> executed.
> 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?

A restraint is a biasing potential that disfavors movement, but does not prevent 
it.  So it is possible that the structure changes.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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