Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
405
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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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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? [closed]
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 ...
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Adding water molecules to a system in LAMMPS
I have a LAMMPS data file with roughly 1000 water molecules, with constituent atoms defined by an atom type (i.e, OW = type 1, HW = type 2), while the molecule itself is not defined explicitly. ...
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Generalization of always accepting box upscaling moves in Monte Carlo for a triclinic box
When you are using Monte Carlo scheme to simulate equilibrium phases of convex hard-core molecules, namely, whose energy is infinite when in contact and 0 otherwise in a standard, cubic simulation box,...
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How is temperature changes implemented in a molecular dynamics simulation?
I copied my question to this community as the advice of a user on Physics SE
MD simulations are always associated with a temperature that represents the natural state of a system.
However, some ...
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Non-Covalent Interaction between drug and DNA?
I am using classical molecular dynamics (MD) to observe a non-covalent interaction between my complex and the DNA, but there is a problem in that the complex interacts with the terminal of the DNA for ...
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Bending rigidity of the nanomaterial from MD simulation
The literature seems to be very diverse in measuring the bending rigidity of the nanomaterial from MD simulation. I have seen people often use this relation from continuum mechanics $$k = \frac{Eh^3}{...
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Protein Molecular Dynamics in water
$$\mathcal{V}(\mathbf{r}^N)=\sum_\text{bonds}\frac{k_i}{2}(l_i-l_{i,0})^2 + \sum_\text{angles}\frac{k_i}{2}(\theta_i-\theta_{i,0})^2 + \sum_\text{torsions}\frac{V_n}{2}(1+\cos(n\omega-\gamma) + \sum^...
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About neigh_modify and dangerous builds in LAMMPS
I am doing a simulation of a 3D LJ system in LAMMPS, where I am heating an already equilibrated configuration at $T^* = 0.3$ to $T^* = 0.4$ for $1000000$ steps then equilibrating the same at $T^* = 0....
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Molecular dynamics method to simulate a simple fluid
I need to implement the molecular dynamics method to simulate a simple fluid that interacts through the Lennard-Jones potential in a 2D simulation. The idea is to explore how the total energy of the ...
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What are the key things I need to learn before I can simulate graphene growth on a metal substrate using LAMMPS? [closed]
I am planning to conduct an MD simulation research on graphene growth on a metal substrate using lammps. I recently learned to form a crystal lattice using lammps. But I have no idea what to look for ...
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Is AIMD classified as MD or DFT?
As far as I know, we need force fields such as Tersoff/Coulomb potentials when performing MD simulations. In AIMD, we use pseudopotentials similar to DFT.
Which method should we classify AIMD to: a ...
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How to get started modeling liquid crystals? [closed]
I am an experimentalist who is interested in getting hands on experience with how simulations play into our understanding of liquid crystal formation. I have tried to read several reviews on the topic ...
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How do I define the density of system? [closed]
Lets' say I have a solid nanomaterial made with N atoms in a simulation box with a volume of V as shown below. In this case, the number density of my material is simply $\frac{N}{Volume\; of \; ...
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Literature applying molecular docking into MD-simulated structures of proteins
This is quite surprising, at least for me, that many papers performed molecular docking of an unsimulated (original) protein structure and MD simulation of a protein in a timescale to check the ...
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Free Graphical User Interface to prepare inputs for LAMMPS
Searching the LAMMPS site, I found some software capable to prepare LAMMPS inputs but they are not free and other software to analyze the output.
I would like to know other package (with Graphical ...
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Software for Molecular Dynamics in Material Science
I would like to know available software that can do Molecular Dynamics (MD) simulations for any type of system, specifically inorganic and organic ones.
The must cited MD packages (GROMACS, AMBER, ...
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Mixed Solvent MD using OpenMM [closed]
I switched to using OpenMM recently and have got up and running without too much of a learning curve.
My general workflow is as follows, using a cloud based GPU to actually run the simulation:
...
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I have a problem with Amber18 configuration at the make install step [closed]
I have a problem installing Amber.
First, I enter the command:
./configure --with-python /usr/bin/python3 --with-netcdf $AMBERHOME/netCDF gnu
Than make:
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2
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1
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How to control the thickness of lipid bilayer with GROMACS
I was trying to perform lipid bilayer MD for my protein based on GROMACS's Membrane Protein Tutorial.
I can successfully orient the protein in the lipid (turquoise) as you can see in the image below:
...
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How to orient the protein for lipid bilayer simulation in Gromacs
I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer.
The domain of the protein looks like this:
Thus I'd like to have the transmembrane part of the protein to be buried in lipid ...
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How to apply FIRE to many atoms where P=F·v seems to be a vector rather than a scalar?
Introduction/Preamble
@SusiLehtola's answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions conjugate gradients, BFGS for energy minimization, Metropolis ...
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Which equation makes it possible to calculate the forces of attraction between a surface and molecules?
Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation?
[Clarification 1] Between a ...
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Appropriate choice of force constant of spring to use for Steered molecular dynamics
As per Boltzmann distribution, the variance, or the fluctuation in length squared is given by $$\sigma^2 = \frac{k_BT}{k_{spring}}$$
Since $k_{spring}$ determines how strong the force I am applying to ...
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Re-parametrization of force fields in LAMMPS
I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
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Density of a spherical droplet of water on top of graphene
I produced a spherical droplet of water by having a box of water (sufficient water molecules inside the box to give the right density of water) on top of a 2d sheet-like graphene. The box becomes a ...
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How to compute 2D density maps in GROMACS?
I have a GROMACS trajectory of MD simulation. I want to make a contour plot of density as a function of two coordinates, namely X and Z. Is it possible to get this using ...
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Long Range Forces in Protein MD Simuation
I am trying to understand how long range forces are calculated under the following situation.
SYSTEM-> Lets say we have a single protein surrounded by water molecules. Now I would like to run MD ...
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Lennard Jones Clusters in Python
I would like to explore the global optimisation of Lennard-Jones clusters in Python. I do not come from a physical chemistry background. I would like to be able to calculate the cluster energy ...
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Water dimer and Free Energy Perturbation (FEP)
I am trying to understand FEP in the context of a water dimer. Let's say I want to calculate $\Delta A$, the free energy change for the following reaction:
$$\ce{H_2O +H_2O\rightarrow H_2O-H_2O},\tag{...
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Scripts to calculate ionic diffusivity
I found several AIMD analyzers to estimate mean square displacement and ionic diffusivity such as pymatgen, mo, vaspkit. I tried some tests and found that the same data set might result in different ...
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Is there a scripted tool to add neutral terminal caps (e.g. NME, ACE) to peptide chains for use with AMBER forcefields?
I have a range of systems consisting of multiple peptide chains, some of which are one residue (i.e. single amino acids), which I'd like to analyse using molecular dynamics and AMBER-flavour ...
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How to generate a polymer in different conformations?
I want to run MD simulations of a polymer, but I want to start from different physical conformations. My question is, how do I obtain these conformations? Is there a software which performs this?
Let'...
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How to assign a "Boltzmann weight"?
I would like to assign a "Boltzmann weight" i.e. $\exp(-E/kT)$ to interactions between particles based on the relative energies. But wouldn't the largest particle-particle energies have the ...
user2026
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Why is my pdb looking so weird? [closed]
I have generated the following pdb file for a polymer:
...
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Langevin vs Nosé–Hoover thermostat
can anyone explain the pros and cons of using the Langevin vs Nosé–Hoover thermostat? I wonder how to choose a suitable thermostat for a system, such as oxide, organic materials.
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Simulated annealing of small protein [closed]
I understand the general concept of simulated annealing and have seen various criteria in papers, but I was wondering if there is a general rule of thumb for selecting a final structure, how many ...
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Martini 3 CG water cluster is not becoming spherical under NVT conditions [closed]
When we put a certain number of molecules in a small cubic box, and put it inside a large cubic box, under NVT simulation, the water cubic box is supposed to be spherical in shape to reach a minimum ...
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What does "dynamics" mean in matter modeling?
As an example, I have seen the phrase "dynamics of proteins" or "dynamics of biomolecules".
The review paper "Protein Dynamics" by J A McCammon has the word in its title, ...
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