Questions tagged [molecular-dynamics]

For questions related to the use of or theory behind classical or ab initio molecular dynamics.

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LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"

I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
Gaurav Maurya's user avatar
3 votes
0 answers
96 views

Include Li+ in force field for Molecular Dynamics

I want to perform some MD including Li+ ions. Specifically I am interested in Li-TFSI (aka Lithium bis(trifluoromethanesulfonyl)imide). I tested both the ATB repository and LigParGen and neither can ...
Marco Di Gennaro's user avatar
1 vote
0 answers
69 views

Temperature damping parameter in lammps [closed]

I need help on how to set Tdamping in MD simulation. In Lammps documentation it is mentioned that the typical value is 100 for nvt, but when I put this value to my ...
Fryad Sharif's user avatar
4 votes
1 answer
177 views

How to do molecular dynamics with different isotopes of the same element?

In this paper, they separated knock-on damage (originating from the collision of the beam electrons with the nucleus of the target atom) from other radiation damage mechanisms (e.g., ionization damage ...
Vladislav Gladkikh's user avatar
5 votes
2 answers
136 views

Do "minimum image convention" and "nearest image" talks about the same things?

I am a little bit confused by the terminologies of Molecular Dynamics simulation. Do "minimum image convention" and "nearest image" talks about the same things? What is their ...
user366312's user avatar
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What is the difference between a "periodic image" and a "nearest image" in MD simulation?

As far as I understand - In MD, when a particle or coordinate moves beyond one face of the simulation box, it reappears on the opposite face as if the box were replicated infinitely in all directions....
user366312's user avatar
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3 votes
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How to maintain constant liquid density during AIMD with NPT ensembe?

I have constructed a solid-liquid interface model with water as the liquid phase. During the AIMD simulation, I used the NPT ensemble. However, I noticed that under the NPT ensemble, the entire model'...
Tieyuan Bian's user avatar
5 votes
0 answers
68 views

Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)

I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
Saha_1994's user avatar
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6 votes
1 answer
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I was wondering how I should interpret the results of my molecular dynamics simulation

I ran a molecular dynamics simulation using forcite dynamics for polymers on graphene and a drug. The dynamics summary shows the total energy, potential energy,kinetic energy, total enthalpy, ...
Jax's user avatar
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Classical MD Simulation for mineralization process

I'm currently trying to simulate the calcium carbonate mineralization process on the surface of nanoparticles. In here, I've already borrowed the classical force-field parameters on here(https://pubs....
Arete's user avatar
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How may I make a slab surface to calculate a thin layer with Quantum ESPRESSO?

I want to know how to calculate the band structure and DOS of a thin layer of iron selenide in quantum espresso. How I can fix the input file? Is it different from Bulk matter or the same? Which ...
Boka Fikadu Banti's user avatar
6 votes
1 answer
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What is the largest number of collective variables used in a metadynamics simulation?

Metadynamics is usually used to construct 1D or 2D free-energy surfaces. There seem to be a few examples for 3D free-energy surfaces: Paper 1: Exploring the Free Energy Landscape of Solutes Embedded ...
BGK's user avatar
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9 votes
2 answers
657 views

How to choose between Molecular Dynamics and Monte Carlo when beginning to simulate either equilibrium or non-equilibrium systems?

Answers to Are MD and MC both able to study both equilibrium and non-equilibrium systems? include lots of examples pointing to "yes". I'm currently faced with a task of modelings small ...
uhoh's user avatar
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3 votes
1 answer
111 views

Are MD and MC both parts of statistical physics?

Are MD (Molecular Dynamics) and MC (Monte Carlo) both parts of statistical physics or is only one of them? If so, which branch (e.g., mechanics, thermodynamics, etc.) and why?
user366312's user avatar
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3 answers
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Are MD and MC both able to study both equilibrium and non-equilibrium systems?

As far as I understand, a system in equilibrium is which already reached its equilibrium state. And, a non-equilibrium system is which hasn't reached its equilibrium state yet. Are MD (Molecular ...
user366312's user avatar
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1 vote
1 answer
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Issues simulating the shape transition of silicon clusters using LAMMPS

I have been trying to write an input file for lammps to simulate the shape transition of a nanoparticle of silicon using multiple potentials to obtain the best structure, which I will compare with a ...
Hadjmohammad Abderahmane's user avatar
2 votes
0 answers
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Interaction energy of two cartesian quadrupoles?

I am looking for a complete description of the interaction of two traceless cartesian quadrupoles. Even just an implementation online would be quite useful. The problem I am having is many of the ...
jheindel's user avatar
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3 votes
1 answer
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Parameterizing a Tersoff Potential in LAMMPS

I am seeking advice regarding a molecular dynamics simulation in LAMMPS of Gallium Phosphide (GaP). I came across a paper by Powell et al. which parameterized a tersoff potential for Ga-P interaction, ...
Bishwajit's user avatar
4 votes
1 answer
77 views

How to study the stability of structure in water and analyze the radial distribution function (RDF)?

Context: If I have a system that consists of 20 structures. During molecular dynamics, these structures can form micelles from my point of view. I would like to do the following: Confirm if the ...
Abd-Elazeem Mohamed's user avatar
3 votes
1 answer
49 views

What is a 'mover' in molecular dynamics?

Movers What is a 'mover' in molecular dynamics? Can you supply me with reading material on 'mover'?
user366312's user avatar
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Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition

While calculating various quantities that involves particle positions ( for example, radial distribution function, mean square displacement etc.) using Molecular Dynamics simulation, the effects of ...
bubucodex's user avatar
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3 votes
1 answer
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Estimate the time between different residues?

Imagine now, I have 5 structures, and I want to estimate the time when the 5 structures are closer to each other at the same time. I thought I could extract the distance between the different ...
Abd-Elazeem Mohamed's user avatar
2 votes
1 answer
58 views

Looking for the OPLS parameters for octanol

I have been looking for OPLS gromacs parameters for 1-octanol, but haven't been able to get it. Doing a quick web search takes me into links for lipidbook, from which I can't download at all from ...
Roshan Shrestha's user avatar
3 votes
1 answer
86 views

NPT Molecular dynamics calculation problem

I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem? This is my code for the heating part. However, the ...
anumoy ganguly's user avatar
8 votes
3 answers
705 views

Duplicate structure in PDB format?

I have a PDB file. I want to duplicate this pdb file automatically instead of doing it manually. For example, if I visualize my PDB, I will find only one structure in (x,y,z). I want to have more ...
Abd-Elazeem Mohamed's user avatar
6 votes
1 answer
248 views

Determine Forces from a Bond Angle Potential

I am looking for a physics based proof for how one applies forces to each of the three atoms in a bond angle potential. I know the general principle that $F = -\nabla \Phi$ if $\Phi$ is your potential ...
Nathaniel Hess's user avatar
5 votes
1 answer
104 views

Time evolution of angle made by the helix with the normal to the plane using gromacs

I am new to the md simulation community. I have a peptide which is helical in a bilayer. I want to calculate the angle of the peptide relative to the bilayer with gromacs. For that, I created an index ...
Anna VDP's user avatar
5 votes
1 answer
159 views

project molecular dynamics trajectory onto phonons by normal mode decomposition

After running the Molecular dynamics(MD) simulation, I'd like to see the excitation of phonons during MD, so I'd like to project the trajectory onto a set of phonons, I've seen some paper use the ...
Jack's user avatar
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9 votes
3 answers
616 views

Can AMBER be used for a molecular dynamics simulation of a Diels-Alder reaction?

I am studying a Diels-Alder reaction of cyclopentadiene and maleic anhydride. I know that AMBER can be used to run MD simulations on proteins, however would I be able to use these small molecules to ...
Joel Daniel's user avatar
3 votes
1 answer
58 views

Could I simulate the applied voltage on the electrode by adding extra electrons in the system?

I try to use molecular dynamics to simulate the half-reaction of the H2O reduction on the Pt cluster. Is it possible to add extra electrons in the system to simulate the reduction process? The Pt ...
Jack's user avatar
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1 vote
0 answers
39 views

Apparent change in bond order of a molecule after an amber simulation? [closed]

I have been following along with this tutorial for simulating a small ligand binding a protein receptor. In both the tutorial and my follow-along (which uses the same commands as the tutorial but with ...
weddegege's user avatar
5 votes
1 answer
93 views

When and why are torques needed in molecular dynamics simulations?

I have seen that many MD simulations compute the torques due to dipole-dipole interactions and other interactions. I understand that there is a torque on a dipole in an electric field. I don't ...
jheindel's user avatar
  • 3,524
3 votes
0 answers
35 views

How to change cell shape during calculations in LAMMPS? [closed]

I was doing some calculations using LAMMPS and wondered if there was a way to change the cell shape during npt or nvt calculations (in the latter, changing the cell shape while keeping the volume ...
Laura's user avatar
  • 967
5 votes
1 answer
121 views

gyration radius of short freely jointed chain with excluded volume

The freely jointed chain model without excluded volume has the following gyration radius, $$ \langle R_g^2 \rangle=\frac{1}{6}\frac{N+2}{N+1}Na^2 $$ where $N$ is the number of bonds and $a$ their ...
Marco Mendívil Carboni's user avatar
3 votes
1 answer
101 views

Energy balance in a molecular dynamics simulation with ghost atoms and periodic boundary conditions?

I am performing a simulation in LAMMPS with granules (DEM) and I had a question regarding the conservation of energy. If an interaction happens where one granule is in the simulation box and the other ...
Devanjith Fonseka's user avatar
5 votes
0 answers
228 views

Is there an effective way to get the energy of a system from a MD trajectory in postprocessing? [closed]

I am trying to get the potential energy of a system at each frame of a molecular dynamics trajectory after running the simulation. My current approach is as follows: Use MDAnalysis to iterate through ...
user avatar
4 votes
1 answer
200 views

Contribution to pressure tensor from water

Cross-posted later on Reddit. I have an infinite CG model of the material solvated in water. I am trying to apply a uniaxial deformation along a particular x-axis; the mdp settings in GROMACS are ...
Roshan Shrestha's user avatar
5 votes
0 answers
36 views

How to get statistical temperature from WHAM? [closed]

I ran a series of replica exchange molecular dynmaics for the different temperatures. I used WHAM to sample metastable states. From the results of WHAM, we can get probabilties ($p $) from the energy ...
이영규's user avatar
8 votes
2 answers
391 views

Silica (α-cristobalite) water system generation

I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
WhiteLeo9's user avatar
  • 183
4 votes
1 answer
66 views

Force field for charged peptide-ion system

I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here ...
Arete's user avatar
  • 193
2 votes
0 answers
58 views

Simulate liquid solvent mobility through a gel polymer electrolyte

I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such a system? Three ...
Marco Di Gennaro's user avatar
4 votes
1 answer
114 views

Effect of trajectory length and resolution on the Residence Time

I have tried to calculate Residence time using the residence time auto-correlation function defined as $$R(t) = \frac{\langle h(0)h(t)\rangle}{\langle h(0)h(0)\rangle}$$ In the calculation, I have ...
anupama's user avatar
  • 121
4 votes
1 answer
115 views

Are thermostat parameters transferable between AIMD and classical MD?

I need to run several large systems using AIMD. I would like to benchmark same phase transition phenomenon using different thermostats (like Nose vs Langevin). For that it is crucial that I pick most ...
ipcamit's user avatar
  • 481
2 votes
0 answers
73 views

CUDA memory Error when using NAMD, mentions cygwin even though cygwin isn't installed? [closed]

I've run into some issues with NAMD that cause me to get the following error whenever I try to begin a simulation run: ...
user avatar
6 votes
1 answer
83 views

Are all molecules under the same peak in g(r) always found in the same solvation shell?

For a liquid, the peaks in $g(r)$ are typically associated with the solvation shells: nearest neighbors, next-nearest neighbors, and so on. However, the $g(r)$ is averaging over many configurations, ...
user avatar
3 votes
1 answer
239 views

Interface between metadynamics and LAMMPS

I am trying to create an interface between the metadynamics and the LAMMPS code. Both the codes are written in two different languages. How can I proceed to create an interface. Thank you
Mangladeep Bhullar's user avatar
3 votes
1 answer
410 views

Difference between two pull codes in gromacs (SMD)

My molecule is aligned along x-axis, and I want to pull this molecule along x-axis with one end defined as the first pull group, and another end as the second pull group. I have two pull codes, which ...
Roshan Shrestha's user avatar
4 votes
1 answer
149 views

How to simulate on a computer dissolution of one substance by another?

Is there any publicly available software to simulate this or some other method to see if one substance can be dissolved by the other (and preferably to see how fast)?
user avatar
2 votes
0 answers
35 views

How to bond two laminates (same material) separated by distance using compressive pressure in LAMMPS?

I would like to simulate the bonding process using compressive pressure for two layers of the same material. Applying a uniaxial strain and using the deform tag in LAMMPS requires PBC in all ...
user6363's user avatar
8 votes
1 answer
248 views

Developing a machine-learned interatomic potential for molecular dynamics

There are few questions in this SE about the advantages/disadvantages of machine-learned interatomic potentials in molecular dynamics, but there is not much discussion on how to make them. I thought ...
user35952's user avatar
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