Problem with 'Thermo and fix ave not computed at compatible times' in LAMMPS
I followed the tutorial (https://github.com/lammps/lammps/blob/develop/examples/KAPPA/in.heat) to compute the thermal conductance of bilayer graphene sandwiched by Al2O3 on both sides along the z...
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How to rotate a periodic structure in LAMMPS?
I want to rotate a periodic structure like this oneby a 10 degrees around a z-axis (perpendicular to the plane) that goes through the center of the simulation box.After writing this in LAMMPS,variable...
View ArticleIs it possible to build a force field that suits all elements based on VASP's...
I have tried to use VASP's machine learning force field calculation during running molecular dynamics simulation with a supercell including some elements of Ti, O, Cu, etc. It does increase the speed...
View ArticleForce fields for generating **Co3O4 and Fe3O4 structures in LAMMPS
I am working on a project that requires generating a large dataset of Co3O4 and Fe3O4 structures under various temperatures and pressures using LAMMPS. The structures will be used for training machine...
View ArticleEnergies from single points vs. AIMD for training Machine Learning Force Fields
I am currently training a force field using machine learning techniques. One way to test the performance of the ML model is to use the force field for a production run (= molecular dynamics) and taking...
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How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of...
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 of...
View ArticleExplain ab initio molecular dynamics like I'm five
In Kashiwaya, S., Shi, Y., Lu, J. et al. Synthesis of goldene comprising single-atom layer gold. Nat. Synth (2024) monolayers of hexagonal Au(111) planes are produced and released into solution where...
View ArticleWhat are the types of ab initio Molecular Dynamics?
I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work?The seminal work by Roberto Car...
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Visualize variation of lattice parameters with temperature after MD
I am interested to plot lattice parameters vs temperature after Molecular Dynamics calculation in NPT ensemble to detect structural phase transition of my system, Ex- So, I am looking for python script...
View ArticleHow the center of mass of a large number of atoms influences the performance...
I'm interested in conducting umbrella sampling between a ligand and the center of mass of a lipid. Initially, I chose the atom numbers for the ligand and all the atom numbers for the lipids. However,...
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Green Kubo Relation
I am calculating viscosity of WCA fluid using the Green Kubo relation. I am also following the paper of Zhang et al. for the Time decomposition method https://doi.org/10.1021/acs.jctc.5b00351 where,...
View ArticleForcefield parameterization techniques
Suppose I have a novel synthetic protein. I want to find the classical forcefields that accurately models the dynamics and thermodynamics of the protein. How do I do that?
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LAMMPS structure rotation
I need to rotate half of the structure 180 degrees, I was able to do this operation but the rotation cannot be made symmetrical, do you have any ideas?commands I used:end result:
View ArticleCheck for steric clashes before doing minimization
Are there already some tools available, or we can code for finding the atoms/residues that can contribute the steric clashes before minimization solve the issue?
View ArticleRelation between force constant of the bonded parameters, time constant and...
I want to understand these things in both intuitive and non-intuitive ways. In some cases, we constrain hydrogens so that we can run molecular dynamics at a higher time step than we normally would,...
View ArticleHow to calculate height of the center of the H2 molecule from surface via ASE?
I have XDATCAR file, i want to calculate graph of time vs height of the H2 molecule(center of the H2 molecule) from surface. bare_Pt_111_2*2_4 1 5.501291 0.000000 0.000000 2.750645 4.764258 0.000000...
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Convergence issue of Temperature Dependent Lattice constant using CPMD
I am trying to find out temperature dependent lattice constant (Silicon) using CPMD (NPT-MD). If I want the lattice parameters at 300 K, should I set temp 300 K in both &cell and &ion card? I...
View ArticleHow to use ASE to combine several MD trajectories into 1 trajectory
I have several continuous MD trajectories. How can I combine them into one trajectory to summarize all?
View ArticleAverage value of lattice parameters from cell trajectory
Is there any post processing tools by which I can get average value of lattice parameters from cell trajectory? For example: I ran 'vc-cp' (CPMD) in quantum espresso (for Silicon) and Si.cel file is...
View ArticleAdding a molecule in AMBER
I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb...
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