How can one create various arrangements of two or more types of atoms (like...
How can I modify the procedure described in this answer to achieve adsorption of two or more types of atoms on a surface, each with distinct coverages?Is there an extension to the described method for...
View ArticleGiven a .gro file of a monomer, how to polymerize it?
I have a structure (.gro) file of a PolyEthylene Glycol (PEG) molecule as shown below. How do I get the corresponding structure file for PEG-20 i.e., a molecule with a degree of polymerization=20,...
View ArticleCalculation of pH in Molecular Dynamics simulation?
I have a system that has 5M aluminum hydroxide (10 molecules) ion [Al(OH)4]- and 5M NaOH (10 molecules) in a box of side length 15 angstroms each. I have 113 water molecules in the system, so that the...
View ArticleHow to convert a SMILES into a LAMMPS or GROMACS input file?
Are there any dedicated Python tools/packages/scripts that help me convert a SMILES structure into an MD coordinate and topology file (both for GROMACS and just the single one for LAMMPS)?Demonstrate...
View ArticleThermal Conductance along the lateral and longitudinal direction
Suppose the left and right leads are both copper rod and the central scattering region is one monolayer graphene sheet. There is no chemical bonding formed between Cu and C atoms. The copper and...
View ArticleThermal vs dynamical stability
Dynamical stability is checked by a phonon curve. Thermal stability is checked by a molecular dynamics simulation. What is the difference between them?
View ArticleMD simulations of liquid isopropanol predicts wrong thermodynamics proprieties
I am using GROMACS to run molecular dynamics simulations of pure liquids, in the NpT ensemble at room temperature and p = 1 atm. My first test was with isopropanol (also known as 2-propanol). I used...
View ArticleSignificant differences between NPT and NVT equilibrated simulations
I am performing a set of classical MD simulations using a type of ReaxFF description to study aluminate Oligomerization. I have performed two sets of simulations, one where the system is equilibrated...
View ArticleAre there scripts available for AIMD?
I need to determine which of two electrolyte is the best for a hydrogen fuel cell. As far as I understand, the first thing to do is to compute their ionic diffusion coefficient and to compare (the best...
View ArticleRestrain a protein to be helical in an MD simulation
I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay...
View ArticleHow to set up the NEMD (Non-Equilibrium Molecular Dynamics) calculation in...
Suppose a benzene ring is connected with copper nanorod on both side along the z axis and they compose the scattering region. On both sides of the scattering region along the z axis, the left and right...
View ArticleCan ACEMD be implemented with OpenPathSampling
Is it possible to implement ACEMD with OPS? I am asking in the context of using NNP/MM models with OPS. The paper "NNP/MM: Accelerating Molecular Dynamics Simulations withMachine Learning Potentials...
View ArticleHow to identify small molecules in a structure without bonds
If I have an XYZ file with a cluster of a dozen of molecules: water, $\ce{O2}$, $\ce{H2}$, $\ce{H2O2}$. A human may easily identify these molecules. But how to do it automatically? I need to identify...
View ArticleHydrogen bonding autocorrelations
I am currently analyzing hydrogen bonding behaviour and kinetics with molecular dynamics simulations. I've been trying to compute autocorrelation functions for hydrogen bonds in a water system. Some...
View ArticleHow to add atom attribute molecule for each layer in LAMMPS?
I want to model several layers of hBN in LAMMPS.First, for two layers, I created a lammps data file from vasp POSCAR using atomsk. It is like this: # hBN_bilayer 3200 atoms 2 atom types 0.000000000000...
View ArticleLost atoms in a lammps simulation
I am simulating the thermal conductance along the z axis for bilayer graphene sandwiched by Al2O3 system. This is my input setting.variable x equal 47.59variable y equal 41.214148966101variable z equal...
View ArticleOptimum number of CPUs to use for an efficient LAMMPS simulation
Are there any rules of thumb to optimize the number of CPUs to perform a LAMMPS simulation of a given size efficiently?For example, there are 32 cores under each node in my computational resource. How...
View ArticleHow can calculate length or coordinate of any molecule in different quantum...
How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming code?
View ArticleHow to use interatomic potential in LAMMPS
This is my input file for the lammps simulation.variable x equal 47.59variable y equal 41.2141489661variable z equal 136.636variable t equal 300.0#Setup parametersunits realatom_style atomicread_data...
View ArticleHydrogen bonding rate of relaxation on molecular dynamics
I am studying the works of Alenka Luzar on the hydrogen bonding kinetics in liquid water. Luzar defines an autocorrelation function c(t) that gives the probability that an hydrogen bond is intact at...
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