VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Nov 18 2015 - 14:08:51 CST
Those types of discontinuities are not uncommon. They are indicative of major structural changes as the result of crossing some energy barrier during the scan. The roughness of the MM PES, however, is a little odd. I would recheck bonds and angles, if you parameterized any, as the dihedral PES is often where trouble with earlier parameters will often show up.
> On Nov 18, 2015, at 8:07 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> Hi VMD users,
> I am trying to parameterize a unnatural amino acid using FFTK. I am at the dihedral fitting stage. I only have one new dihedral to fit.
> What I find strange is that the QME plot has discontinuities. I ran the Gaussian jobs with 5 degree step and 2 degree step, but both the times the discontinuities persisted. Is this normal, or has someone else had this issue as well?
> I have attached the QME plot here.
> Best regards,