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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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What is the byproduct of a reaction between copper sulfate pentahydrate, sodium carbonate, and elemental iron when heated?

This is entirely a curiosity of mine that requires an answer and not an actual experiment or documented reaction, so far as I can find. I was looking for a professional to inspect/clean a wood stove ...
2
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1answer
39 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 ...
5
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1answer
67 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 ...
2
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1answer
57 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 ...
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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 ...
7
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1answer
74 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
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1answer
138 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 ...
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1answer
97 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 ...
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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:/...
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0answers
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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 ...
7
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1answer
176 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. ...
4
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1answer
145 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 ...
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1answer
689 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 ...
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1answer
576 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 ...
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1answer
201 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 ...
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1answer
55 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 ...
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0answers
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What is the difference between the following two pseudopotentials for Na?

Please see the attached snapshots taken from cp2k website. In the first case (Na-q1) the core charge is 1, number of core state is 3 and number of valence states is 13; while for the second case (Na-...
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2answers
122 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 ...
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173 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 $\...
2
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1answer
167 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,...
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3answers
455 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, ...
6
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1answer
259 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 ...
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2answers
235 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 \...
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1answer
201 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 ...
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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 - ...
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1answer
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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 (...
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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,...
4
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1answer
244 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 ...
13
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2answers
508 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 / ...