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1
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2answers
40 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
votes
0answers
24 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
votes
0answers
18 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
87 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
86 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
1answer
51 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 ...
1
vote
1answer
38 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, ...
0
votes
1answer
59 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
votes
0answers
43 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 ...
0
votes
0answers
50 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 ...
1
vote
1answer
57 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
votes
1answer
43 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??
0
votes
1answer
47 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
votes
1answer
104 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 ...
0
votes
1answer
84 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
votes
2answers
147 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
votes
1answer
129 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?
4
votes
4answers
139 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
52 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
99 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 ...
3
votes
1answer
153 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
votes
0answers
161 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
votes
1answer
143 views

Implementation of the MARTINI force field

Given an input parameters for the MARTINI force field such as: ...
0
votes
1answer
129 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
181 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
243 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
292 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
701 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
203 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
169 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
592 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
104 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
725 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
105 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 ...
1
vote
0answers
31 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 ...
3
votes
1answer
131 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 ...
13
votes
4answers
5k views

Do currently available GPUs support double precision floating point arithmetic?

I have run the molecular dynamics (MD) code GROMACS on a Ubuntu Linux cluster consisting of nodes containing 24 Intel Xeon CPUs. My particular point of interest turns out to be somewhat sensitive to ...
2
votes
1answer
65 views

Progression of molecular dynamics simulation sizes

I'm looking for literature on the progression (year on year, or more fine-grained if possible) of Molecular Dynamics simulation sizes. By simulation size I mean number of atoms, time step, total ...
2
votes
2answers
100 views

Maximizing distance between point particles

I have a situation where I am trying to maximize the distance between some point particles. For example, I have a periodic simulation box that is 100 Å$^3$, and I am putting in 361 particles. ...
5
votes
1answer
155 views

Periodic BC for Multigrid in MD

I know that this question might be very specific and maybe nobody will know the answer, but this is probably the only community where I could find an answer: So, as part of my master's project, I am ...
4
votes
1answer
210 views

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 ...
3
votes
2answers
89 views

What is the difference in accuracy between fully QM atomic simulations vs QM + classical?

If I want to do a very accurate simulation of a molecular system (e.g. 2 hydrogen atoms), then I'll want to use something like diffusion Monte Carlo to determine the energies of these atoms in ...
4
votes
2answers
175 views

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 ...
1
vote
0answers
54 views

Parameter determining argon phase

Currently I am running a molecular simulation in the $NPT$ ensemble to determine the phases of argon using a Lennard-Jones potential. Mainly I use the radial distribution function to determine solid, ...
5
votes
1answer
293 views

What is the scaling or order of molecular dynamics (MD) simulations?

Often in computational science, we talk about the scaling or order of a particular method ($\mathcal{O}(N)$, $\mathcal{O}(N^2)$, $\mathcal{O}(N \log N)$, etc.). I am having a really difficult time ...
5
votes
1answer
459 views

Minimum image convention for triclinic unit cell

The minimum image convention (MIC), see for example a short note of W. Smith, is often used in molecular dynamics or monte carlo simulations of periodic systems with an orthorhombic unit cell. For ...
2
votes
1answer
239 views

In molecular dynamics (MD) simulations, how is particle number density computed in practice?

I have been reading a recent paper. In it, the authors performed molecular dynamics (MD) simulations of parallel-plate supercapacitors, in which liquid resides between the parallel-plate electrodes. ...
11
votes
3answers
4k views

What are the advantages and disadvantages of the particle decomposition and domain decomposition parallelization algorithms?

I am running molecular dynamics (MD) simulations using several software packages, like Gromacs and DL_POLY. Gromacs now supports both the particle decomposition and domain decomposition algorithms. ...
8
votes
2answers
696 views

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 ...
4
votes
2answers
173 views

Tools/solutions for visualization of molecular simulation trajectories?

I have so far been using VMD to create visualizations of molecular trajectories. However, I find myself not entirely satisfied with the quality of the resulting animations—when you want to do ...