Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
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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 ...
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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 ...
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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?
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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 ...
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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 ...
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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 ...
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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, ...
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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 ...
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What is a 'mover' in molecular dynamics?
Movers
What is a 'mover' in molecular dynamics?
Can you supply me with reading material on 'mover'?
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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Apparent change in bond order of a molecule after an amber simulation?
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 ...
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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 ...
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How to change cell shape during calculations in LAMMPS?
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 ...
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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 ...
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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 ...
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Is there an effective way to get the energy of a system from a MD trajectory in postprocessing?
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 ...
mertvy
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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 ...
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How to get statistical temperature from WHAM?
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 ...
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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 ...
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How to use VMD to visualize a coarse-grained model
Disclaimer: I am new to VMD and molecular dynamics.
I am currently working on a simulation of a very basic coarse-grained model of DNA (or rather ssDNA because every base pair is a single bead). This ...
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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 ...
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simulate liquid solvent mobility through 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 system?
Is MD a ...
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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 ...
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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 ...
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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:
...
Roshan Pathak
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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, ...
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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
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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 ...
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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)?
Ya Y
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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 ...
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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 ...
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Av. pressure in NPT equilibration of highly concentrated system [closed]
I'm relatively new to MD simulation, and am studying a highly viscous system of very concentrated aqueous biphasic systems of two different electrolytes. The higher-concentration systems are ...
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Ab-initio molecular dynamics of liquid systems: best tools and resources
I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential ...
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Regarding Simulation Equilibration process
I have gone through this article attached, where in the methodology section they mentioned about the simulation being started with NPT ensemble keeping the box constant for 2 ns. And, I have a ...
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What causes atoms to not interact in LAMMPS? [closed]
I am trying to set up a LAMMPS simulation for depositing graphene on a nickel substrate. I am using ReaxFF forcefield. However, the carbon atoms just pass through the nickel atoms. Can anyone help me ...
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Adding vacuum region in PACKMOL
How do you specify a symmetric vacuum region (along z) above and below an inorganic substrate using PACKMOL? I tried to increase the box size in .pdb and use that in packmol. But it changes the box ...
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Can an atomic structure created after a simulation performed at 251K in LAMMPS be initialized directly to 268K in a separate simulation? [closed]
I have a combined mW water and FCC111 Aluminium substrate model to study ice nucleation and adhesion. This simulation is performed at 251K which is the temperature for the actual real-world experiment....
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Thermal conductivity in GROMACS?
Is there any way we can calculate thermal conductivity in GROMACS? I can see the equilibrium Green-Kubo method algorithm, or non-equilibrium Muller-Plathe algorithm implemented in LAMMPS, but don't ...
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Ovito dislocation analysis
How can I append my pipeline in Ovito?
I tried to append DislocationAnalysisModifier with Selected atom:
...
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How to apply colors and graphics to VMD from Tcl?
I have a collection of pdb files (15), and I want to basically apply the same visualization settings on each one of them and render the image.
I want the above settings, with a certain, resolution ...
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which atom_style to be able to simulate a heating a CNT in water in edpd model? [closed]
I am trying to use energy conservative dissipative dynamic (edpd) model to simulate heating a flexible CNT which is floating inside a liquid (water). Using create_atoms command I am creating my liquid ...
