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
7
votes
0answers
346 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
311 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
94 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
86 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
104 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
44 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
40 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 ...
