Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
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Applicability of GFN-FF force field and other xTB methods for dynamics of ions in water
I am working on a project involving water clusters with ions in them. One of the problems that I ran into quite early on was that good forcefield parameters are not available for highly charged ions ...
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How to build amorphous Al2O3 using the AIMD method implemented in VASP?
I want to build amorphous $\ce{Al_2O_3}$ with the AIMD (ab initio molecular dynamics) method implemented in VASP.
I'm thinking of this process in three steps:
Build initial supercell
Melt
Quench
I ...
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Mixed Solvent MD using OpenMM
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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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 ...
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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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DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?
The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
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Contribution in action from collisions for a gas?
So if I write the action for a gas:
$$ S = \int (T -U) dt \tag{1}$$
where $T$ is the kinetic energy and $U$ is potential energy.
I suspect there is a constant term (which does not affect the equations ...
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How to calculate small and wide-angle X-ray scattering spectra for the hydration shell restricted by a distance radius criteria
My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many ...
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How do you Select a Time Step for Molecular Dynamics Simulations?
It seems there is a general agreement among the practitioners of Molecular Dynamics that 1fs is a fairly reasonable time step, with shorter time steps being required for materials with higher ...
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How to analyse structure factors calculated from a mixture of isotropic amorphous substrates
I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...
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References for Electrostatics Calculations Used in Molecular Dynamics
I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
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Calculating bending modulus of a CG model of a surface from MD simulation
I have built a CG (Martini) model of a 2D Nanomaterial. For now, I want to calculate its bending rigidity. As far as I know, the bending modulus can be computed by making the nanomaterial infinite - i....
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Apparent conservation of potential energy in NPT simulation?
I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
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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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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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How do I define the density of system?
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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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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Regarding use of GCMC to add water molecules
I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
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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 ...
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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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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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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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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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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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How to get started modeling liquid crystals?
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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I have a problem with Amber18 configuration at the make install step
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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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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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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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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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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Literatures applying molecular docking into molecular-dynamics-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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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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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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