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3
votes
1answer
83 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
105 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
76 views

Implementation of the MARTINI force field

Given an input parameters for the MARTINI force field such as: ...
0
votes
1answer
82 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
86 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
131 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 ...
1
vote
0answers
96 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 The current options are outdated (for instance, Jmol uses Java).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
209 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
129 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 ...
2
votes
3answers
118 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
4answers
242 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
93 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
268 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
51 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
27 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
99 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 ...
0
votes
0answers
27 views

Generating topology (angles and dihedrals) from bond connectivity

Is there a tool out there that will take a file of atomic coordinates or bond connections and generate an output file with the angle (bending) and dihedral (torsion) connectivities? It needs to work ...
10
votes
3answers
2k 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
54 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
95 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 Ă…$^3$, and I am putting in 361 particles. ...
5
votes
1answer
89 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
165 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
74 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
140 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
50 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
158 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 ...
4
votes
1answer
252 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
171 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. ...
10
votes
2answers
2k 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
444 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
130 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 ...
12
votes
1answer
206 views

Complexity of MD simulations

I'm new to molecular dynamics (MD) simulations. What is the complexity of a molecular dynamics simulation in terms of simulation time? In other words, if I want increase the simulated time from 10 ...