Questions tagged [molecular-dynamics]

For questions related to the use of or theory behind classical or ab initio molecular dynamics.

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Determining bond angle from infrared spectra?

Looking at some historical data about water, I noticed that people were determining bond angles from infrared spectra. How is this done? Aside from having a bunch of absorption frequencies indicating ...
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Creating Amber/CHARMM style force field potential for energetic materials using DFT

What are the basic steps and methodologies used in creating inter-atomic force field potential for CHARMM/Amber style for energetic materials with the help of DFT? What are the best possible free ...
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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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What's a quick way to get a molecular bond length using a Newtonian model?

Can anyone spare me a clue on this? I'm a self-taught student of Molecular Geometry trying to learn more about methods in modeling. After some extensive reading and study, it felt like it should be ...
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How to calculate diffusion coefficient from MSD graph using GROMACS?

In GROMACS I have used the command below to calculate mean square displacement (MSD) over time, ...
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1 vote
1 answer
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I have a force in eV/Angstroms. How do I convert it so that the speed I calculate is in Angstroms/second?

How can I express speed in Angstroms/second after application of a force that's in eV/Angstrom (given the mass, original velocity and time elapsed)?
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Is it possible to build a force field that suits all elements based on vasp's machine learning result?

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 ...
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What are the similarities between MD and MC in the case of protein simulation?

As far as I understand, both MD and MC simulation methods use Force Fields. Are there any other similarities between them?
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Radius of gyration and aggregates

I have performed a MD simulation using GROMACS for a system of 100 caffeine molecules in water. It is expected caffeine form aggregates. I have calculated the radius of gyration for the simulation ...
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Calculating the Diffusion coffecients from Trajectory file in ASE

I plan to study the Diffusion-Coefficient of my simulation outputs, for this, I want to use ASE. Sadly I am not entirely sure of how to proceed, has anyone done this and if yes, please share your ...
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How to run 2nd generation CPMD in CP2K?

I believe CP2K by default implements Born–Oppenheimer MD. I have seen many recent papers that use 2nd generation Car–Parrinello MD using CP2K. But I couldn't find any direct way of switching to 2nd-...
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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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Is the energy due to external electric field included in gromacs energy?

I have a Gromacs NVT simulation with a constant external electric field using the option "electric-field-z = 1.5 0 0 0". When calling gmx energy -f (...).edr to calculate the potential ...
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Simulating autoionization of small molecules using DFT or AIMD

From what I’m reading, simulation of autoionization in liquid substances is hard to do using gas phase DFT or AIMD[1][2][3]. I am using ORCA to do my work and I must confess that I’m shocked to see ...
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MD calculations for RO in the materials studio software

To study the SiO2, polyamide and two layer SiO2-polyamide as the membranes in the reverse osmosis desalination of saline water I used the Materials Studio software to model the systems. My question is ...
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4 votes
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Why does the temperature fluctuate severely during the AIMD using an NVT ensemble?

I am trying to raise the temperature of my model and keep the temperature at 300K, with an NVT ensemble and Nose-Hoover thermostat. I am doing this job with VASP, here is the ...
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Atomic Simulation Environment (ASE) is unable to read a big trajectory file

The problem that I face is the ASE software can't read the trajectory file and throws this error ValueError: buffer is smaller than requested size. My assumption is ...
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How can we test the force field (parameter) for a complex?

I built a force field for a complex. How can I check if the force field is working well or no? I did a short molecular dynamics using AMBER only for the complex using the parameters I built. It worked ...
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2 answers
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Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?

I have a question related to parameterize Lennard-Jones interaction to get sigma $\sigma$ and epsilon $\epsilon$ to include in amber force field to do the Molecular Dynamics. I searched a lot, they ...
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Periodic boundary conditions or spherical potential?

I was wondering whether you know if there is any sort of literature discussing whether periodic boundary conditions or spherical potentials could be better or worse for QM/MM or MM simulations, their ...
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Where to find/ to get Tersoff and Stillinger Weber Potentials for MD simulation using LAMMPS

I'm trying to calculate the thermal properties of Silicene with hydrogen and halogen atoms. My problem is that, there's seems no available potential for Tersoff and Stillinger Weber Potential. and I'...
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Calculate the atomic charge for transition metal using RESP?

I calculate the atomic charge using restricted electrostatic potential (RESP) and compute with the Hartree Fock method. This method is OK for organic compounds, but for complexes that contain ...
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8 votes
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Young's modulus from MD simulation

I have a coarse-grained model of a surface which is almost planar/flat in 2D. Now, I want to compute some of its mechanical properties to test it. Young's modulus is one of the properties that come to ...
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10 votes
1 answer
93 views

Contact Angle (water droplet on a surface)

I have built a CG model of a surface on which I want to place a water droplet (some water molecules), and calculate the contact angle. Has anyone done similar work with gromacs (MD simulation)? First, ...
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4 votes
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Gromacs generate forces using .pdb topol.top and .mdp file [closed]

Given the start configuration (.pdb), topology file (topol.top) and run file(water.mdp). I want to generate the forces on atoms. I tried, using: ...
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What does the shape of the radial distribution function(RDF) indicate?

From my understanding, generally in the RDF plot for liquids, the value of $g(r)$ goes to a maximum near the first solvation shell and then goes to a minimum and then slowly tapers off to the value of ...
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3 votes
2 answers
75 views

How to quantify the lattice distortion from XRD?

In real crystals, the atoms may not always sit at their ideal lattice sites. How to quantify this lattice distortion? Based on my understanding from X-ray diffraction books, the Radial Distribution ...
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Is it incorrect to use a NVT ensemble for Non-equilibrium MD simulation?

I am getting some conflicting results on this topic while searching for literature online, so I am asking this question here with respect to a simplified experimental setup. If we are trying to ...
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Diffusion coefficient as a function of distance from the position autocorrelation function

I am trying to understand if my idea for the computation of diffusion coefficient as a function of distance is right or not. So, the diffusion coefficient as a function of distance is given by, $$D(z) ...
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6 votes
1 answer
101 views

Understanding derivation of discretized FIRE algorithm

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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Basics of configuration initialization strategies used in molecular dynamics? [duplicate]

This answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions conjugate gradients, BFGS for energy minimization and Metropolis Monte Carlo (and the) the ...
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Basics of numerical energy minimization techniques used in molecular dynamics?

The question below describes my plan to make a basic molecular dynamics calculation using a Python script rather than a canned, self-contained program. There seems to be three parts: a model of the ...
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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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17 votes
4 answers
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I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?

I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations. In brief I would like to know what types of simulations work ...
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6 votes
1 answer
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How do biaxial potentials like the Gay-Berne potential work?

I am trying to understand and implement the Gay-Berne potential, but I do not quite understand how one goes about constructing them. I am following this paper to parse through the idea. I understand ...
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115 views

Gromacs generate charges for a .pdb file

I have a .pdb file containing water molecules. ...
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6 votes
0 answers
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How to calculate and plot the electrostatic forces in a .pdb file

Given a pdb file that looks like the following: ...
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15 votes
1 answer
163 views

What are the advantages of (semi)-empirical force fields over Machine Learning Potentials?

I am currently working with ReaxFF, an empirical reactive force field that can describe chemical bond forming and breaking. The main advantage over ab initio methods are of course the greatly ...
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14 votes
3 answers
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Can DFT simulate chemical reactions?

I was wondering, can you simulate the chemical reaction between two or more molecules using DFT? If not, what numerical method is usually used for this?
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8 votes
1 answer
112 views

Parameterize a complex that contains Transition metal (Build Force Field)?

It is a general question. I know, but I need some help. I am interested to parametrize a complex that contains transition metal like Ru and Pt etc. Furthermore, I will use this Force Field to do ...
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5 votes
0 answers
61 views

Vibrational density of states from a single snapshot?

The typical way that I know of for calculating the vibrational density of states is to take the Fourier transform of the velocity autocorrelation function for a trajectory. Is it possible / meaningful ...
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6 votes
0 answers
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Dynamical features in molecular dynamics

I would like to know how to compute dynamical properties/correlations like self-intermediate scattering function and probability distribution function of displacements (I think it is so called van ...
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6 votes
0 answers
34 views

Molecular Dynamics to study crystallographic phase transition

I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose.. which has easily available tutorials/example input ...
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7 votes
1 answer
328 views

How to generate a .tpr file from a .pdb or .xyz file in gromacs

I have a .pdb file for a single frame of water in a box. I need to calculate and analyse the electrostatic field for choosing a viable atom in this particular ...
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6 votes
1 answer
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Is it possible to simulate the intercalation of hydrogen nanobubbles?

Is it possible to simulate the intercalation of hydrogen nanobubbles into 2D layered materials using first principles calculations such as Density Functional Theory? Would this require a multi-scale ...
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7 votes
0 answers
53 views

Can Markov State Models based on short-term non-equilibrium datasets also capture the dynamics towards equilibrium?

I am non-specialist who is new to the field of computational physics/biology. I have a few questions about the relevance and effectiveness of Markov State Models (MSM) in capturing the dynamics ...
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11 votes
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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 on water clusters with ions in them. One of the problems that I ran into quite early on was that good parameters are not available for highly charged ions such as $\ce{Al^3+}$...
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10 votes
1 answer
116 views

Very high negative pressure in MD simulation of liquid quenching

I am trying to prepare turbostratic carbon structure from an initial random carbon sample with a density of 1.8gcm$^{-3}$. The initial sample image is attached here: The problem is the high negative ...
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10 votes
1 answer
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What does the slope in the viscosity vs shear acceleration graph from non-equilibrium MD signify?

In finding out the viscosity of a system with non-equilibrium MD using GROMACS, an acceleration is given to the system due to which, the velocity profile changes. This change in energy is used to ...
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9 votes
0 answers
55 views

Generalized Born implicit solvent models and pairwise descreening

It seems almost all the common implementations of Generalized Born (GB) implicit solvent models (in Amber, OpenMM etc) use the "pairwise descreening" approximation, which is described in ...
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