Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
133
questions
7
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0answers
28 views
Creating Interatomic Potential for Lammps using DFT
What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
6
votes
0answers
24 views
How do I build and run a simulation of water molecules in NAMD?
So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
4
votes
1answer
69 views
Simulating polymers using cellular automata?
I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
9
votes
0answers
47 views
What kind of physical properties can be calculated from the “Valence Electron Density” data of a molecule?
I'm wondering specifically in the context of calculating physical properties from valence-electron-density data using DFT, MD, and or ML (machine learning).
7
votes
1answer
109 views
How to address the errors on Automated Topology Builder?
I was trying to get the charges and the topology file for this molecule (C28H58O7S8).
But I get the following error despite using the right number of hydrogens.
Error:
Semi-empirical geometry ...
12
votes
1answer
52 views
What does this temperature & total free energy profile mean (obtained from VASP NVT molecular dynamics simulations)?
In order to obtain molecular dynamics (MD) simulations trajectory for computing phonon dispersion relation at finite temperature, I performed NVT MD simulation using VASP for my target system.
Here is ...
4
votes
0answers
18 views
Can we calculate the intermembrane protonation state?
I want to know the protonation state of the intermembrane subunit of a protein.
For that, I need to know the pH, so given that small molecules can cross the lipid bilayer, could we assume intracelular ...
15
votes
6answers
2k views
How do I simulate the interaction between two atoms?
I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
7
votes
1answer
46 views
How to calculate the volumetric energy density of a molecule?
I am trying to store hydrogen in a hydrocarbon.
The example can be taken as cyclohexane ($\ce{C6H12}$) which is in a hydrogen-rich state. Its hydrogen-lean state is Benzene.
I want to calculate the ...
7
votes
1answer
50 views
How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?
When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
3
votes
1answer
31 views
Missing residues in ATB downloaded pdb/rtp files
I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md)
Two files are available: a PDB file and a topology ITP/RTP file.
The name of the ...
11
votes
2answers
61 views
What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?
I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
8
votes
2answers
98 views
Large pressure fluctuations in molecular dynamics
I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level.
For example, I set the pressure at 1 bar and it averages ...
13
votes
1answer
147 views
Minimum image convention for non-orthorhombic unit cells
I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells.
I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...
4
votes
0answers
33 views
What will be the cohesive energy of an alloy in LAMMPS?
The cohesive energy of a pure material is generally termed as the energy of a unit cell divided by the number of atoms. what will be cohesive energy of an alloy in LAMMPS? I am running LAMMPS for $\ce{...
12
votes
1answer
154 views
Analyzing MD trajectory: molecule orientation
I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field.
There are two order parameters that are used to ...
4
votes
1answer
49 views
Calculating Velocity autocorrelation function for Binary Diffusion Coefficient
I have been attempting for some time to evaluate the binary Diffusion coefficient of argon in a gas mixture with neon. From the literature, this property can be measured using the velocity ...
10
votes
1answer
95 views
How do I calculate the radial distribution function from the centre of mass of unit cell in GROMACS?
I am simulating a droplet of water with GROMACS. The droplet consists of about 200 TIP3P water molecules and is placed near the center of a large, mostly empty box (...
6
votes
1answer
65 views
Molecular dynamics: how to pack system for desired density
I'm trying to perform ab-initio MD on polymer system.
I've built single chain of polycarbonate (PC) with the length of ~40 angstroms and now I'm building initial configuration. I've calculated how ...
8
votes
1answer
63 views
Understanding the rigorous bridge between atomistic and coarse-grained simulations
I am currently reading this paper by Noid et. al. on the rigorous bridge between atomistic and coarse-grained simulations.
In the paper, he defined a linear map from the atomistic coordinates and ...
6
votes
0answers
35 views
How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?
I am trying to reproduce the 2D SAXS interference pattern of bulk water via ab-initio MD methods as shown in the figure below:
The main aim is to recreate figure (a) via averaging MD configurations ...
12
votes
1answer
87 views
Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance
I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm.
I first load a default system of particles (alanine-dipeptide in ...
7
votes
1answer
81 views
Using LAMMPS for a small system
I want to run a classical molecular dynamics simulation on silicane using LAMMPS. Since I don't have access to any HPC nor do I have a powerful desktop PC, I'm planning on making the system small. By ...
5
votes
1answer
39 views
Bulding host-guest polymer system for molecular dynamics
I'm thinking of running MD simulation of poling process (heating and cooling in external electric field) of host-guest polymer system: organic chromophore in polymer matrix (PMMA or polycarbonate).
So,...
11
votes
1answer
78 views
Unable to recreate data for benzene from paper in GROMACS 2020.5
I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
10
votes
1answer
143 views
What novel drugs are developed via CADD?
Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery.
Which drugs that have ...
7
votes
1answer
161 views
Molecular Dynamics Simulations in VASP
I want to run molecular dynamics (MD) simulations with VASP for Mg2Si to investigate the simulation time vs ENCUT and KPOINTS, ...
3
votes
0answers
137 views
Error in GROMACS for adding ions to a solution
I am following Justin Lemkul's GROMACS simulation given on this website here for GROMACS.
I believe I have followed the process to the T. I would like to mention that in the "Generate Topology&...
9
votes
2answers
436 views
Is the dynamics of a peptide molecule Markovian?
I was wondering if the underlying dynamics of a full atomistic trajectory of a peptide molecule are Markovian.
Note added after the first two answers:
I assumed that they were Markovian, as they are ...
9
votes
2answers
102 views
Starting configuration for a molecular simulation
When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results?
The book Computer Simulation of Liquids suggests putting the molecules on an ...
11
votes
3answers
396 views
Which ensemble to use for a molecular dynamics simulation?
Does it matter which ensemble you use for a molecular dynamics simulation? Shouldn't they in principle give the same results? Why, historically, was it hard (and desirable) to develop simulations in ...
11
votes
1answer
98 views
Selection of appropriate Langevin damping parameter for MD of solid metal
I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this.
I have previously used the ...
8
votes
0answers
30 views
Lone pairs in CHARMM for molecular dynamics
I have a substrate that has a Br-C bond. In CHARRM the line below is included in the .str file:
...
7
votes
1answer
101 views
cp2k conserved quantity changed when restart NVT MD?
The details are descripted elsewhere, but got no answer for days, so I post it here for help.
As title said, I noticed a relatively big change in conserved quantity and don't know why.
I've upload ...
12
votes
1answer
314 views
Compute RDF between COMs of two selections (or groups) using GROMACS
I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...
12
votes
1answer
91 views
Recent developments in QM/MM for Molecular Dynamics
I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
10
votes
0answers
76 views
Using Molecular Dynamics as an experimentalist to study how much plastic work is converted to heat, does anyone have any comments on our paper? [closed]
When you load a metal and the deformation results in permanent plastic deformation, the input work should be converted into heat and thus dissipate. But for about 100 years people have struggled to ...
13
votes
1answer
160 views
Visualizing MD generated electron density cubes as trajectories
During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
8
votes
0answers
56 views
Periodic polarizable QM/MM embedding
Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
7
votes
0answers
70 views
How to effectively simulate high density systems in GROMACS?
I have a system with a dense liquid solvent and a polymer solute. I have inserted all the molecules randomly using gmx insert-molecules and then did the energy ...
9
votes
1answer
61 views
Algorithmic description of implementing path integral molecular dynamics?
Suppose I have a functioning molecular dynamics package for classical MD. I want to extend this code to run path integral MD. I know that a surprisingly small number of new features need to be ...
8
votes
1answer
114 views
Are there other kinds of stability of materials? How to demonstrate that with computation approaches?
I have known some kinds of stability of materials, such as:
Mechanical stability;
Dynamical stability;
Thermal stability
In particular, they can be studied with first-principles computational ...
7
votes
1answer
76 views
For ergodicity, what is the significance of the R value and slope?
I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to ...
7
votes
0answers
107 views
How to build amorphous Al2O3 using the AIMD method implemented in VASP?
I want to build amorphous Al$_2$O$_3$ with the AIMD (ab-initio molecular dynamics) method implemented in VASP.
I know that two procedures should be taken into account, namely
1st: melt
2nd: quench
...
6
votes
0answers
34 views
How can I quantify the uncertainty of thermal molecule properties in molecular dynamics simulations?
When doing molecular dynamics simulations, there are countless sources of error (i.e. approximations and numerics).
Molecular dynamics can be used to determine intrinsic thermal properties such as ...
9
votes
1answer
85 views
Methods to handle non-ergodic systems with Molecular Dynamics
Given the large difference between simulation timescales and the timescales on which we normally interact with ensembles of molecules, the time average of a molecular dynamics simulation does not ...
13
votes
2answers
484 views
Classical Monte Carlo vs. Molecular Dynamics
Both Classical Monte Carlo (MC) and Classical Molecular Dynamics (MD) simulations are used to perform simulations of ensembles of molecules. These MC calculations are calculating thermodynamic ...
6
votes
1answer
86 views
Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?
I'm looking for a simulation of different water models (TIP3P, SPC/E, TIP4P, water models with flexible bounds) where the differences in simulation speeds on a common architecture are really seen. ...
9
votes
1answer
95 views
Is there a way to understand pi-pi interactions through GROMACS?
I have two polymer molecules with benzene rings as a part of them. I would like to understand how the interactions between them influences the solvability of the polymer in a non-aqeous solvent. I ...
7
votes
0answers
39 views
Reaction simulation at specific temperature, pH and pressure [closed]
Can we design metal organic frameworks, layered double hydroxide using LAMMPS? How?
I want to synthesize a metal organic framework or such materials, and I want to ask if I put two to three chemicals ...
