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 ...

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77 views

Beowulf Cluster For MD simulations

What would you recommend as an all-in-one cluster management software for a Beowulf cluster? We have about 7(most of them are 8 core machines and 1 is a 48 core machine) very good compute nodes in our ...
3
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0answers
34 views

Is resampling more accurate than block average for statistical analysis of data?

I'm working in laboratories where molecular dynamics data are almost always analysed usign block average as stated in the famous Allen and Tildesley book. We divide the datas in blocks of size $M$ on ...
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1answer
22 views

Modeling Coupling: vibrational,rotational, etc

I am trying to figure out how to deal coupling. I am trying to model a polymer chain. I have to deal with the angle between adjacent angles, dihedral angles, and vibration. I am able to compute all ...
1
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3answers
59 views

Choosing the correct Ewald sum parameters

I'm currently working with a system where the long range Coulomb interactions are described with the Ewald summation method. I am using DL_POLY Classic. The Ewald summation method used is described ...
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0answers
44 views

Adding a new potential term to DL_POLY Classic

I am using DL_POLY Classic to simulate CO2 behavior in upper mantle conditions. I am trying to use a recently new forcefield for this system. In this FF, the potential energy between two atoms in the ...
9
votes
1answer
105 views

Ways to start ab initio MD from classical MD

I am running molecular dynamics simulations of water for testing purposes. The box is quite small, if you ask a guy running classical MD, and relatively large, if you ask a DFT guy: I have 58 water ...
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0answers
76 views

Why not solve molecular dynamics trajectories exactly?

The basis of Molecular Dynamics simulation is the integration of newton's equations of motion: $$\frac{F}{m} = \frac{d^2r}{dt^2}$$ I understand that there are various methods based on Taylor's ...
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1answer
43 views

Creating dense random configuration in for molecular dynamics

I am creating a random configuration of particles for a molecular dynamics simulation, where I would like to guarantee a certain density. The strategy is as follows: choose randomly the positions of ...
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0answers
77 views

Maxwellian distribution of velocities with Shake algorithm present

I am writing a code to perform hybrid monte carlo molecular dynamics. To do this, I need to have a code to initialize the velocities of all particles according to a maxwell distribution. The code is ...
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0answers
30 views

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 ...
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43 views

Available Software packages for setting initial configuration

I have just started learning Molecular Dynamics using dl_poly_classic and analysing trajectory using nMOLDYN. For this purpose, I want to construct a micellar system of (say of single micelle) in my ...
3
votes
2answers
264 views

Fortran code for Ewald summation

I am trying to write a code to calculate the potential and forces, for the same using ewald summation.For this purpose, the formula for potential and force I have used is : $$ U = U^{(r)} + U^{(k)} ...
0
votes
1answer
98 views

Unfolding folded trajectories for Diffusivity calculation - MD

I have just started using dl_poly classic to work in Molecular Dynamics simulations. It produces a HISTORY file which records the trajectory after applying boundary conditions. Now, here I don't ...
2
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0answers
119 views

Molecular dynamics: Lennard-Jones forces in 2D system

As I am new to all these stuff I would like to verify whether my procedure is correct. I need to calculate the Lennard-Jones potential, potential energy of the system and the forces. The procedure ...
1
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2answers
84 views

Estimation of time taken to reach steady state in an MD simulation of Poiseuille flow

I am trying to do a Molecular Dynamics Simulation of a complex fluid, confined between solid surfaces. I would like to find the flow rate as a function of fluid film thickness, $h$, for a plane ...
0
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0answers
35 views

Optimization of a molecular dynamics coarse grain model

I am trying to optimize a model I develop for molecular simulation, however, I have zero experience in optimization and I need some guidelines in approaching the solution. I basically do not know ...
0
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0answers
25 views

thermostatting tip4p water model

I have written a tip4p water code, but am having issues trying to figure out the proper way of thermostatting and measuring the temperature. From hand calculating velocities outputted by lammps, I ...
6
votes
1answer
143 views

Generating random numbers for long molecular dynamics simulations

I've written a basic 2D Langevin dynamics simulator in C++, for a particle in a potential, solving the equation: $$M\ddot{X} = - \nabla U(X) - \gamma M \dot{X} + \sqrt{2 \gamma k_B T M} R(t)$$ This ...
7
votes
1answer
159 views

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 ...
3
votes
2answers
230 views

periodic boundary conditions for triclinic box

I am trying to do analysis on a data set of atomic coordinates generated form lammps. I simulated an alpha glycine crystal in a triclinic box. The box vectors look like the following, where xy,xz,and ...
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1answer
43 views

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, ...
3
votes
1answer
647 views

How do I generate maxwell-boltzmann variates using a uniform distribution random number generator?

I am doing a molecular dynamics simulation. I need to assign initial velocities to the atoms. I want to assign the initial velocities which follow the maxwell-boltzmann distribution. How do I ...
0
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0answers
119 views

MD simulation - Water Vapour

I wanted to know the procedure of starting up a water vapor calculation in LAMMPS. I want to calculate properties of water (i.e. in vapor state) at a higher temperature than 100 Celsius. Currently I ...
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0answers
64 views

How to keep velocities in check in molecular dynamics simulation?

I am trying to make a very simple molecular dynamics simulator with Reflective Boundary Conditions. I am assigning the initial positions in a cube randomly while making sure they are not too close to ...
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1answer
83 views

How can I make velocity verlet algorithm more stable?

The answer to this question implies that reducing the time step would make it more stable. However I have tried reducing the time step but the system is still unstable(the total energy increases to a ...
0
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1answer
93 views

How to generate movie of the simulation done in LAMMPS? [closed]

I simulated nanowire deformation using LAMMPS and visualized it using VMD in Centos 6.5. But I'm not able to generate .jpg image file or the simulation movie. How can I proceed??
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1answer
53 views

Unexpected behavior, values tend to converge instead of fluctuate. (MD)

I am writing a molecular dynamics program to create an lattice and populate it with atoms/molecules. These then are given random velocities and the system is initialized. Then throughout time the ...
2
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1answer
161 views

Is Langevin thermostat/equation correct when trying to model time-dependent behaviour of a molecule?

I've been taught that when simulating a biomolecule in thermal equilibrium, it's best to use the Langevin thermostat - an algorithm which produces a trajectory, which is a realization of a stochastic ...
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1answer
167 views

Molecular Dynamics : Phase transition Lennard Jones potential

I'm doing molecular dynamics of $N$ bodies interacting through Lennard-Jones potential. I'm studying the hysteresis phenomena in the phase transition solid-liquid and liquid-solid. Which parameters ...
0
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2answers
257 views

Molecular Dynamics: Diffusion with PBC

How can I implement the computation of the diffusion coefficient $D$ using periodic boundary conditions (PBC)? I use molecular dynamics of a set of $nboby$ particles with positions $pos(3,nbody)$ in ...
2
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1answer
156 views

Are there companies which create commercial molecular dynamics / monte carlo simulations? [closed]

I would like to know if there is a commercialization of simulations? Or is it only in academic usage?
5
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4answers
147 views

Removing non-determinism from molecular dynamics code

I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing ...
2
votes
0answers
70 views

Algorithms for adding hydrogens on a molecule

I want to add hydrogens to some linear polymer molecules (polyethylenes). I know some working methods like using PyMOL internal function h_add. This method works, but hydrogens are added at distances ...
0
votes
1answer
164 views

PQR files make from pdb2pqr are different to GROMACS

I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce pqr, with topol.top taken from pdb2gmx and use it to produce pdb file, then use pdb2pqr. Which one is ...
4
votes
1answer
195 views

Increasing thread number degrades performance

I have a problem with parallelization and the brownian dynamics (molecular dynamics) code that I am using. We have our own home-grown framework at the university, and recently we've made the change ...
0
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0answers
218 views

how to visualize velocity from Lagrangian particle tracking method

I have few particle's position and velocity information as a function of time. Particle is following a trajectory path, while doing so, one particle may disappear, other particle may appear. Particle ...
0
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1answer
161 views

Implementation of the MARTINI force field

Given an input parameters for the MARTINI force field such as: ...
0
votes
1answer
146 views

Non-deterministic/probabilistic molecular dynamics simulations

I'm looking for a piece of software for performing molecular dynamics simulations with the following specifications: required: well published (as in there are papers citing it in one or more ...
3
votes
1answer
277 views

Molecular dynamics: how to calculate interfacial tension [closed]

How can one determine the interfacial tension at a solid-liquid interface using molecular dynamics? What are some good articles on this topic?
3
votes
4answers
321 views

Finding a molecular dynamics visualization library for C

I asked this question over at stackoverflow, and got blasted for it. I am currently working with legacy MD code written in C that my university uses, and haven't moved to a more modern library like ...
2
votes
0answers
472 views

Optimizing display of millions of triangles per second

I am working on a web-based molecular visualization program for a research project (e.g., one that can display XYZ and PDB files). The current options are outdated (for instance, Jmol uses Java). My ...
6
votes
3answers
1k views

Finite-size effects in molecular dynamics simulation

I will be blunt: this is an old exam question of a course that covers Molecular Dynamics (MD) and Monte Carlo (MC) simulations. Explain how to determine the severity of finite-size effects. My ...
2
votes
3answers
232 views

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 ...
3
votes
3answers
199 views

Reproducibility in molecular dynamics trajectories

Let's say I have two molecular dynamics (MD) simulators, A and B, which implement the following interface: $$ \left\{\vec{x}_i(t = 0), T_i, t \right\} \rightarrow \left\{\vec{x}_i(t), \vec{F}_i(t) ...
3
votes
5answers
790 views

Finding the correct Molecular Dynamics library

I just started working on some Biophysics research, and I was looking around for a good MD library to use. There is one right now at the university set up in C, with openMC parallelization, but the ...
1
vote
1answer
108 views

Molecular dynamics simulation: fluctuating dipole model implementation

I'm conducting a molecular dynamics simulation for silica. Some time ago I turned to the fluctuating dipole model, and after much effort I'm still having problems implementing it. In short, all ...
8
votes
2answers
1k views

Genetic algorithm vs conjugate gradient method

I am trying to optimize some force-field parameters in a molecular framework so that the result of simulation comes as close as it can to the experimental structure. In the past, I have written a ...
1
vote
0answers
152 views

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 ...
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0answers
32 views

Simulation of asymmetric structures (occupancy = 0.5) unstable

I am trying to simulate a metal-organic framework in LAMMPS using the UFF potential. It's working quite well for some structures where all molecules have an occupancy of 1. However, when I have a ...
4
votes
1answer
151 views

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 ...