The molecular-dynamics tag has no wiki summary.
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84 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
19 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
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0answers
16 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 ...
2
votes
1answer
56 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
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0answers
15 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 ...
5
votes
2answers
168 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
44 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
71 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. ...
4
votes
1answer
51 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 ...
3
votes
1answer
109 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
60 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
102 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 ...
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0answers
22 views
How can I know the distance of an atom from the heli's axis in GROMACS? [closed]
I am looking at the structure of iota-carrageenan double-helix.
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0answers
40 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
106 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
141 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
113 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. ...
6
votes
1answer
1k 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
276 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
107 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 ...
10
votes
1answer
166 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 ...
