Questions tagged [molecular-mechanics]

For questions pertaining to classical force-field methods in computational chemistry, including molecular dynamics simulations using such force fields.

8 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
7
votes
0answers
340 views

Cloud-based molecular modeling software

I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
7
votes
0answers
303 views

How are the angle bending parameters defined in the MM2 force field?

I am currently looking through the openbabel implementation of the mm2 forcefield. While I understand most of the implementation, I don't get the definition of the angle bending parameters (see https:/...
4
votes
0answers
92 views

Molecular (infrared) vibrations: General relationship between molecular mechanics force constants and harmonic frequencies (in internal coordinates)?

In molecular mechanics method simple molecules, say symmetrical tri-atomics (H$_2$O), have potential energy surface governed by distances $r_1,r_2$ and angle $a$ like $V (r_1,r_2,a_{121}) = K (r_1 - ...
2
votes
0answers
50 views

Calculate activation energy of intermolecular displacement on a nano particle

I'm simulating a nano particle and wish to calculate the activation energy of the reaction where an atom is displaced from one point on the lattice to a neighboring void( might be at higher energy ...
1
vote
0answers
52 views

Understanding the gaff2.dat proper dihedral parameters

I have a project where I'm trying to program my own force field, and I decided to use the AMBER gaff2.dat force field parameters. However, I am really struggling parsing the gaff2.dat file when it ...
1
vote
0answers
101 views

Calculating the free energy of separation in AMBER

I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of ...
0
votes
0answers
39 views

Normal (Regular) or Inverted Terms?

I have a question on the order of the spin-orbit molecular states. I understand how to find the terms that split from a parent molecular state in a diatomic molecule. But my question is on how to find ...
0
votes
0answers
34 views

Gaussview GMMX grid seach: job completed before going through all the structures

I am recently using the GMMX add-on in gaussview to conduct conformer search. I was using the grid search method and the progrom suggested the number of structures is 729 (See picture below). I ...