VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed May 23 2018 - 21:19:54 CDT

Wow, ok that definitely makes sense and makes my life easier with the ring and cage structures we study. Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Wednesday, May 23, 2018 3:39:44 PM
To: McGuire, Kelly; vmd-l_at_ks.uiuc.edu
Subject: RE: Scan Torsions

Hi Kelly,

You only actually need to rotate bonds to +/- 180 if the bonds are freely rotateable. That is most definitely not the case for some of your bonds, since rotating some of your bonds past about 45 degrees (? I'm totally guessing here) will break a bond in QM, which is irrelevant to your parameterization effort. What you do in those cases is sample more closely than the FFTK defaults over a smaller range (so maybe +/- 45 in 5 degree increments), and use FFTK to fit the shape of the energy surface around the minimum.

-Josh

On 2018-05-23 13:16:00-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

I am on the Scan Torsions step of the FFTK plugin, and my molecule has a carbon cage (amantadine). Some of the dihedral scans struggle

to finish. I set the scan to do +/- 180 for all of the dihedrals. I'm wondering what the best procedure for a cage type molecule would be

for a torsion scan. Most of them finish with the default MP2/6-31(d), but about 5 of them either end with the internal coordinates error, constraints

errors, or just stops without errors. However, if I change to HF/6-31(d), they finish with normal termination. I don't fully understand the difference between HF

and MP2 other than MP2 is a hartree-fock approximation but with an electron correlation energy correction. How much would it change my results on this

step if I used HF instead of MP2, or is there a better way to get the scan torsion to work for a cage molecule? Thanks!!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602