[gmx-users] evaluation of simulated frames by procheck

[Seera Suryanarayana]

Dear gromacs users,

I have done simulation of peptide with 28 residues length for 100ns. I have
used the OPLS force field. My peptide is disordered peptide and two of its
regions have been modeled by using modellar. After modelling I have checked
the steriochemical  properties of the peptide by procheck and their
G-factor value is greater than -0.5. After my simulations I have taken some
of the frames randomly and checked the steriochemical properties of them by
procheck and  I got G-factor value is less than -0.5. If the G-factor value
less than the reference value i.e -0.5 the structure has to be validated. I
got less G-factor values for my all frames. Now my question comes here. As
I didn't get greater G-factor values than reference values, is my
simulation not valid? For your information all ramachandran angles are in
allowed regions. And also suggest how to defend my simulation is valid.

Thanks in advance
Surya
Graduate student
India.