VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon Mar 22 2021 - 22:48:09 CDT

Hi Daniel,

I inquired within the group, and the consensus is that there are multiple ways to approach it and that it doesn’t necessarily matter which way you go. If you can’t run the full scan, that’s fine! Just do, say, +/-90 deg., or even +/-60 deg. Any state with really high energy ( > 8-10 kcal/mol) is irrelevant anyway. The goal is just to generate conformations that are likely to be accessible in a typical MD simulations. If you do multiple scans, just make sure there aren’t duplicated conformations that would over-weight them.

Best,
JC

On Mar 21, 2021, at 7:28 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz<mailto:dfel694_at_aucklanduni.ac.nz>> wrote:

Hi all,

I'm optimising a set of dihedrals for a strained alkane. It's a 2,2,3,3-tetramethyl substituted cyclopropane, and one of the high penalty dihedrals is Me-2-3-Me.

What I'm unsure of is which methyl group/s to set for the dihedral scan for this term: Trans or cis to the first methyl? The start angles are ~0 and ~140 degrees respectively, and I doubt that a +/- 180 degree scan would run smoothly. Should I scan both to +/- 90 degrees and use both to construct the PES?

My other concern is that the methyls are quite close to each other so they would interfere sterically no matter what I choose. But they obviously can't be removed as they're part of the dihedral definition.

Daniel Fellner BSc(Hons)
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326