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Questions tagged [molecular-dynamics]

Molecular dynamics simulations aim at solving the equations of motion of the atoms belonging to a molecular system using explicit time propagation and taking into account the effect of temperature on the atomic velocities (as opposite to geometry optimization). The interatomic forces can be described in classical (MM), quantum (QM) or mixed (QM/MM) frameworks.

Molecular dynamics simulations aim at solving the equations of motion of the atoms belonging to a molecular system using explicit time propagation and taking into account the effect of temperature on the atomic velocities (as opposite to geometry optimization). The interatomic forces can be described in classical (molecular mechanics, MM), quantum (quantum mechanics, QM) or mixed (QM/MM) frameworks. A number of constraints can be applied to part of the system in order to simplify the problem. For instance, intramolecular bonds are often constrained in MM simulations.

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Molecular dynamics simulation of water vapor?

I'm trying to do MD on water vapor. As I know there exists some water models for liquid water, such as SPC,SPC/E,TIP3P, but will they also apply to vapor state of water? And what's the difference of simulations of liquid and vapor water?
dofine
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energy drift in molecular dynamics

I hope the following question will not be perceived as to vague. I am trying to ask the question directly, without going into too much information regarding my code. I am currently developing a molecular dynamics code for a custom application, as…
user3225087
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NVE MD simulation of inert gas: Problem maintaining equilibrium

I have been trying to simulate a simple problem of taking about 100-1000 Ar molecules in a NVE (fixed vol, energy) system with equal speed but randomized velocity, and evolving them to obtain a Maxwellian speed distribution. I am choosing a Lennard…
Sankaran
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What is the most accurate molecular dynamic simulation method

First of all, I want to say that I am extremely new to MD simulations, so I apologize for any of these questions if they appear to be something that should be well known. I know that the classical type of picture that MD packages such as Gromacs…
chase
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Difficulty with possibly the simplest MD simulation

I am going ahead with asking what might appear as a debugging question. But,I am looking for something conceptual that I might have missed, and this question is somewhat related to my previous question: NVE MD simulation of inert gas: Problem…
Sankaran
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How can I easily verify my molecular dynamics simulation?

I have written a molecular dynamics simulator with a single potential function (lennard jones). I initialise the temperature of the system using a Boltzmann velocity distribution. Is there a standard way of verifying that it works? E.g. some…
RNs_Ghost
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Neighbor lists in overdamped Langevin MD simulations

The following question is about the implementation of molecular dynamics simulations with neighbor lists. In cases where the paths of individual particles are (i) stochastic and (ii) somewhat rough, without well-defined velocities, it seems…
TLDR
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Effect of Periodic Boundary condition in Pair Distribution function

When we simulate a bulk molecular system using molecular dynamics in (say) NVE ensemble (microcanonical), we apply some periodic boundary conditions (PBC) to avoid surface effects. What effect does this have on quantities like Pair Distribution…
user35952
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Proper handling of 1-2 1-3 1-4 bonded neighbors in long range electrostatic solver

I have been wrestling with how to properly deal with bonded (1-2 1-3 and 1-4) particle neighbor interactions, or whether they have to be dealt with, in the long range electrostatic solver codes (PME, SPME, etc). For instance, in the short range…
user3225087
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Accurate force-field for MD

I am still a fairly new graduate student, and I am having trouble simulating a metal-organic framework. I am currently using UFF (I implemented it for LAMMPS), and it works well for some MOFs, but does not give empirically accurate results for…
Nick
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Compute either only the attractive term or the repulsive term in Lennard-Jones

The Lennard-Jones potential is typically expressed mathematically as: $$ V(r) = 4 \varepsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^{6} \right] $$ where: $V(r)$ represents the potential energy as a function of…
user366312
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Langevin Thermostat and overdamped Langevin Equations

I'm having some difficulties understanding the Langevin thermostat (MD). In my notes, there is written that the Langevin equation is $$ m\dot{v} = F - m\gamma v + f_R, \tag{1} \label{1}$$ where $f_R$ is the random force. Then, to prove that by using…
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Rigid and flexible ZIF-8 framework

What are the differences in parameters in the force field for MD simulation study of RIGID and FLEXIBLE ZIF-8 framework?Is the electrostatic interaction term present in the rigid one?
Piyali Mukherjee
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How to integrate numerically Nosé Hoover equation?

In NVT molecular dynamics, Nosé Hoover thermostat is a method defining an extended system. I can understand perfectly how the Nosé Hoover differential equations are derived (Frenkel&Smit's book). However, when it comes to practice, I have no idea…
Damien
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How to control temperature in NVE molecular dynamics

I want to simulate a molecular system at a certain temperature. It would be best if it could be implemented by NVT molecular dynamics. However, if one were to use a NVE simulation (like velocity Verlet), how could I fix the temperature, or let the…
Damien
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