having trouble to get the NPT working
I am currently encountering challenges in successfully conducting NPT simulations in LAMMPS for a triclinic cell persistently remain unchanged throughout the NPT simulation.my input file is:# Units and...
View ArticleHow to use martinize.py?
I have been trying to get the CG representation of a basic octane molecule. The pdb file is as follows:ATOM 1 C1 BUT 1 2.142 1.395 -8.932 1.00 0.00ATOM 2 C2 BUT 1 3.631 1.416 -8.537 1.00 0.00ATOM 3 C3...
View ArticleSpeed of atom from kinetic energy of molecule
What is the velocity of each hydrogen atom in an H2 molecule, given a kinetic energy of hydrogen molecule is 0.12 eV, when expressed in angstroms per femtosecond and assuming equal velocities for both...
View ArticleEliminate the entropic contribution in the free energy of dimerization...
For my set-up to compute the free energy of dimerization between two molecules in a solvent using umbrella sampling, I can see that there is an entropic contribution since I have used distance as a...
View ArticleError with running GROMACS with SLURM
I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows:#!/bin/bash#SBATCH -Jgromacs_cpu #SBATCH -Axxxxxxxxxxxx #account...
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Equilibrating Surface Temperature Through NVT Ensemble Ab Initio Molecular...
In my AIMD simulations with the NVT ensemble at T= 300K (Nosé–Hoover thermostat)for a Pd (111) surface (2*2, 6 layers) and vacuum sizes of 14 Å and 18 Å, All other INCAR tags are same(only NGZ for 14Å...
View ArticleGeometry of H2O in the v=1 vibrational state for AIMD simulation
This is a follow-up to my recent question: Algorithm for finding the v=1 state of an H2O moleculeI want the geometry (atomic positions) of the H2O molecule in the v=1 state. How are initial...
View ArticleWhat is the best way to optimize molecules with 8000 atoms. This includes...
My molecule includes C,H,O,N,Si
View ArticlePrerelaxation before AIMD with VASP
I am investigating a bulk structure by ab initio molecular dynamics (AIMD) implemented in VASP.I was wondering, how to choose the initial geometry (= POSCAR file) to run the AIMD simulation. In the...
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Velocity autocorrelation function for molecular dynamics trajectory
I have a 1 ns long molecular dynamics trajectory of 884 molecules of water, and I am trying to compute the velocity autocorrelation function using MDAnalysis to analyze the GROMACS output files.I have...
View ArticleHow to compute the Elastic Modulus of a molecule using GROMACS?
Say we take the basic example of a PEG molecule (PolyEthylene Glycol). What is the fundamental physics for computing the Elastic Modulus or the Young's Modulus from the Molecular Dynamics (MD)...
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Controlling Initial Velocities in NVE Trajectory Simulations with VASP
"I've determined the initial velocities of the surface following its equilibration at 300 K in the NVT ensemble. Now, I aim to conduct AIMD (NVE ensemble)with the metal surface (initially defined...
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My CHARMM IC table generation has caused hydrogen to bond to two carbons. How...
As above, I am attempting to generate an IC table for decanoic acid using CHARMM (version 48b1) so I have a minimized geometry. I have attached my build.inp script and the stream file I have written. I...
View ArticleAdvantages/Disadvantages of Qeq over Drude polarizable model?
For classical Molecular Dynamics (cMD) simulations, the usual methodology is to use force fields (FFs) with fixed point charges (examples include CHARMM, AMBER and Gromos). However, this approach means...
View ArticleHow to write the REBO force field
I want to use the REBO-CHO force field to study graphene oxide using lammps. But I don't know how to create the input file with the parameters by reading the article or if there is a tutorial or...
View ArticleSolvation_analysis subpackage for MDAnalysis multi-atom solute
I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input.I am...
View ArticleModelling excited states using classical MD simulations
My question is related to the question here but not exactly the same. The studies which have looked into the excited states of molecules have generally done it by parameterizing the ground-state and...
View ArticleHow can a harmonic constraint be added between two groups in one direction...
As a new user of NAMD, I am seeking assistance regarding a specific task. I intend to pull a LIGAND from outside to the center of a lipid using NAMD. To achieve this, I have utilized the colvar module...
View ArticleHow can I specify the direction of motion in the colvars file?
I am doing umbrella sampling in NAMD and I want to control the distance in the colvars to be in one direction. Is there any possibility?
View ArticleQuestion about Constructing Supercell Layers for MD Simulations for...
I am a newcomer to MD simulations,so my questions may be at a basic level,but I appreciate your understanding.I would like to simulate solid-solid phase transitions using MD simulations.To begin with,...
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