Questions tagged [molecular-mechanics]

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

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14
votes
2answers
638 views

Molecular mechanics force fields for metals?

I know of several general molecular mechanics methods suitable for metals, including Dreiding and UFF. I know it's difficult to get many things right for such classical treatment of inorganic / ...
12
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1answer
225 views

Verifying data acquired from a molecular dynamics simulation

This question is about verifying a system simulated with MD. I am currently building a model of a two phase gas-liquid system, where I initially have $\ce{N2}$, $\ce{CO2}$, $\ce{Ar}$, $\ce{He}$ and $\...
10
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3answers
847 views

Why might a planar, conjugated molecule be higher in energy than a nonplanar system?

I have a small molecule (23 atoms) for which I want to verify parameters in a molecular mechanics force field. My first step is to look at the potential energy as a function of the dihedral angle, ...
9
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1answer
1k views

How to perform molecular dynamics simulations of charged systems?

The GROMACS official documentation (see here) states that a system with non-zero total charge will yield an error: System has non-zero total charge Notifies you that counter-ions may be required for ...
8
votes
2answers
1k views

The time scale of calculations in computational chemistry

Is it possible to determine or get a range of the time required for a specific calculation with knowledge of the type (MM or QM), class (semi-empirical, ab initio or DFT), the degree of theory (MP, CI,...
7
votes
1answer
411 views

Amber solvatebox: How do I remove water that has traveled away

I used Amber's solvatebox function with a small polypeptide and tip3p water with a distance of 15 angstroms between the molecule and the edge of the box. After I ran dynamics, I tried to view the ...
7
votes
1answer
140 views

How do water models fit into force field methods?

What I Understand: In molecular mechanics, it is recognised that molecules tend to be composed of units that are structurally similar in a vast array of environments so atom types are defined from ...
7
votes
1answer
342 views

Molecular Hamiltonian of Helium hydride ion

Currently, I am going through Quantum Simulation of Helium Hydride Cation in a Solid-State Spin Register. I am not a chemist but rather a computer scientist hence having trouble following the paper. ...
7
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0answers
348 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
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0answers
313 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:/...
6
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2answers
160 views

Force Fields and units

I am a math student trying to implement a simple force field in python for determining the energy of a small molecule and trying to minimize it in order to find a stable configuration. I was wondering ...
6
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1answer
151 views

How to use the calculate velocity correlation from VanHove correlation?

I am trying to derive an expression for the velocity correlation function $C(t) = \langle \mathbf{V}(t) \mathbf{V}(0)\rangle$ from the VanHove correlation: $$ G(\mathbf{r},t) = \frac{1}{N}\left( \...
6
votes
1answer
338 views

How to write an entire trajectory into a single PDB file?

I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library. With VMD if I do ...
6
votes
1answer
178 views

How to Calculate Lennard-Jones Parameters from TDDFT?

I am trying to develop parameters for AMBER force fields and to calculate Lennard-Jones parameters for the $\ce{Fe^3+}$ ion. I did a deep search and found that the best way to do this with a high ...
5
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2answers
252 views

Why we can't see 3-d structures of certain compounds on PubChem?

It's common to read statements like one given below on PubChem: Conformer generation is disallowed since MMFF94s unsupported element. What's the meaning of the statement, and why are certain ...
4
votes
1answer
1k views

Physical meaning of (negative) pressure in molecular dynamics simulations

Lately I have been simulating a system in an NPT-ensemble where $N$ is constant and $P$ and $T$ are coupled to a Berendsen barostat/thermostat. The system is cubic and periodic in all directions. I ...
4
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1answer
205 views

What is the “curse of dimensionality” in molecular dynamics?

The 'curse of dimensionality' or the 'bottleneck problem' in molecular dynamics is explained in page 5 and 6 of Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods by Dominic Marx and Jurg ...
4
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0answers
96 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 - ...
3
votes
1answer
300 views

pka from molecular dynamics

How can one calculate pKa values from first principle calculations, static or dynamics? I have encountered some works using CPMD where people try to find pKa values from -(i) constrained Molecular ...
3
votes
1answer
244 views

Convergence of spectra calculated from molecular dynamics trajectories

How can we check whether or not the power spectra (vibrational density of states) calculated by taking the Fourier transform of the velocity auto-correlation function (VACF) from a molecular dynamics ...
2
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1answer
69 views

Understanding water models?

I generally work on fluid flow, so some basic concepts in chemistry are new to me. Work I'm doing requires use of molecular dynamics (MD) to do classical potential simulations of water–NaCl systems ...
2
votes
2answers
419 views

Estimate Partition Function from a simulation

I have a system and I've carried out a long molecular dynamics simulation over it. I would like to estimate the partition function $Z.$ Theoretically, one would compute: $$Z=\dfrac{1}{N!h^{3N}}\int \...
2
votes
1answer
603 views

Radial pair distribution function (VMD). How to define it for a water NaCl system with multiple Na and Cl?

I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly ...
2
votes
1answer
260 views

How can absolute binding free energies be calculated?

In the calculation of binding free energies, such as between a protein and a ligand, I learned that absolute values cannot be obtained from simulation (such as taught in this lecture, slide 2). Rather,...
2
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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
1answer
114 views

Generating PDB file from electron density without force field minimization

Is there a step-by-step tutorial on how to generate a PDB file from an electron density file (*.ccp4)? For my current project, I am trying to take some statistics ...
1
vote
1answer
303 views

Lennard-jones cut-off

I am using a Lennard-Jones potential in a computer simulation and I was wondering if i should place a cut-off for low distances since the potential blows up quickly making the calculations quite ...
1
vote
1answer
59 views

Building a solid-liquid interface

I am trying to build a solid-liquid interface to be simulate using molecular dynamics. Since, I would be using ab initio molecular dynamics (cpmd or cp2k), I need the minimum cell dimensions. Please ...
1
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0answers
92 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
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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
1answer
68 views

Fixing incongruities in PES Scan [closed]

I tried to parameterize a particular x-y-z-t dihedral angle of novel molecule using a Quantum Mechanical scan, but I got the strange result below. The energy changes sharply around 130° and $E_\text{...
0
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1answer
91 views

A question about geometry of benzenetetrol

In the 3d conformation of 1,2,4,5 - benzenetetrol, how could i determine the direction to which hydrogen atoms of hydroxyl groups would point? and if there were tertiary butyl groups in positions 3 &...
0
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1answer
76 views

Model of London forces and Hydrogen Bonding; the question is carried on forward, partially, as a personal question, from another question [closed]

Does Model of London forces and Hydrogen Bonding are themselves complicated and require multiple sub-models and assisted theories to explain its correctness. I asked this question in the form (...
0
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0answers
48 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
45 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 ...