[gmx-users] Difference in omega angles!!

[Justin Lemkul]

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

-- 
==================================================

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

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

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================