Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
171
questions
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Very slow performance for an OPLS-AA methanol simulation
I am running a methanol simulation with a topology I obtained from Tinker for OPLS-AA, at 298 K and 1 bar. This is my .itp file:
...
3
votes
3answers
74 views
How to make input script file for nanoparticle using LAMMPS?
Hope you're all doing well. I am a student of Doctorate in Beijing Institute of Technology. We are working on a project "DNA Regulated Nanozyme". and we intend to build an interaction ...
10
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2answers
112 views
Quantum chemistry in external electrostatic field?
Which quantum chemistry methods can be used in an external electrostatic field? Also which software supports that? I'm interested in anything from semiempirical (eg XTB) to DFT (eg ωB97, B3LYP-D3) ...
8
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1answer
150 views
Calculating compressibility from a molecular dynamics simulation: what is meant by "volume fluctuation"?
I am trying to calculate isothermal compressibility from an NPT molecular dynamics simulation, but am not that experienced and don't know how to use an expression from a paper to do it.
The part that ...
6
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1answer
68 views
How to fix "bad timestep" error in LAMMPS?
I'm working on this project where I have to simulate a gold nanoparticle impact in a gold plate, my script is:
...
6
votes
1answer
59 views
Radial distribution function for trajectories or time frame?
In many scripts I came across, I saw for the calculation of the RDF, both the
trajectory and the individual timeframe also have been used.
Can anybody help me with understanding how they are different ...
5
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0answers
54 views
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 ...
5
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0answers
34 views
What's the pair correlation function? And what information we can read from it?
This question is related to this VASP tutorial, in which the pair correlation function (or radial distribution function: RDF) is utilized to justify whether the solid silicon is melt by AIMD (ab-...
4
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0answers
48 views
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 ...
7
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2answers
214 views
What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?
I've been studying MD and more specifically about Car-Parrinello Molecular Dynamics and I'm not entirely sure if I understood the meaning behind the minimization.
This is the way I understand it: The ...
5
votes
1answer
54 views
What is the equilibrium bond length for a Lennard-Jones potential?
If I have $\epsilon$ and $\sigma$ can I calculate equilibrium distance $r_e$ in one run? What I have tried is to put $V = \epsilon$ and bring out the $r$ from the formula, but it seems not solvable. ...
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37 views
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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How do I model drug diffusion from polymeric matrix?
I have been redirected to this forum from Chemistry SE.
My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
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0answers
38 views
Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme?
Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
6
votes
0answers
40 views
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 ...
7
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0answers
74 views
Setup for 4-point flexible water model
I tried to search online if there are examples or suggestions on how to setup a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc. but there's no clear example on ...
6
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0answers
85 views
How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?
I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...
11
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3answers
185 views
Limitations of pairwise additive forcefields
What are some of the limitations on the use of a pairwise additive forcefields in classical molecular dynamics simulations?
6
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0answers
44 views
Back-mapping Martini 3 coarse-grain to all-atom representations
I have a $10\mu s$ trajectory with 10,000 frames that I would like to backmap to atomistic representations so that I can compare my ensemble to experimental measurements.
I am using MartiniTools for ...
5
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1answer
61 views
List of software for creating random multi-component alloy inputs for DFT or MD
I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.
6
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1answer
53 views
Where can I find/generate force-field parameters for common inorganic anions in water?
I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
16
votes
2answers
818 views
Flying ice cube effect in molecular dynamics?
I am trying to understand what exactly the flying ice cube effect is, and how it manifests itself in MD simulation.
From what I have read about it, I see that as we run certain forms of velocity-...
10
votes
2answers
408 views
How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?
I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...
10
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1answer
110 views
What does vacuum signify in the simulation box after the simulation?
While carrying out constant volume simulations, I've observed that sometimes when the gaseous molecules come closer from their initial spacing, an empty space is created in the box. As I should ...
14
votes
3answers
397 views
MD: How to estimate number of timesteps to converge a property
If I want to equilibrate a NPT system until a property reaches its equilibrium value (let’s say the volume V), what is the common practice to have a rough estimate of the total simulation time ...
8
votes
1answer
56 views
LAMMPS input card in an NVIDIA GPU
I want to simulate the attached model for a Cu NP in Ar using my GPU, but I got erratic results. All looks well when I simulate it in my CPU with the command:
...
9
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0answers
48 views
Molecular dynamics with surfaces
I want to run molecular dynamics with LAMMPS, the aim is to simulate a platinum surface with a gas phase consisting of simple molecules. I would like to use periodic boundary conditions in order to ...
7
votes
1answer
90 views
Where to get Tersoff and SW potentials for LAMMPS
I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
7
votes
0answers
108 views
Is it possible to experimentally verify this collision rate formula?
Background
Let's say I have the $i$'th gas molecule with velocity $\vec v_i(t)$ at time $t$. To find the net displacement $s_i$ we integrate with respect to $t$:
$$ \vec s_i = \int_{0}^{t} \vec v_i(t')...
6
votes
1answer
92 views
Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?
I am currently doing a simulation of the behaviour of various sizes of water droplets (~100-1000 water molecules) in vacuum. I am using NAMD with the spherical boundary conditions to keep the droplet ...
6
votes
0answers
42 views
Molecular dynamics to reproduce dispersion interactions
I'm trying to simulate the behavior of chromophore molecules incorporated into a polymer under an external electric field.
I've tried to use classical molecular dynamics (GROMACS) but it's unable to ...
10
votes
1answer
263 views
How should I generate a radial distribution function (RDF) for an MD trajectory with python?
I am attempting to analyse the radial distribution function (oxygen to oxygen) for a ~400ps simulation on a droplet of water (MD done with NAMD). I am using the python library MDAnalysis to do this. ...
3
votes
0answers
85 views
Practical way to reduce pressure fluctuations in molecular dynamics? [closed]
I am running a test setup in LAMMPS. I am using $4000$ atom hcp system with MEAM potential.
The system need to be at equilibrium at $\pu{10K}$ and for this I am giving initial velocity at $\pu{10K}$ ...
5
votes
0answers
33 views
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 ...
6
votes
1answer
65 views
Secondary structure information at each frame in a VMD trajectory
I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list
to calculate the secondary structure ...
8
votes
1answer
318 views
I generated Wannier centers but am having trouble understanding how they relate to the atoms in my system: there are more Wannier centers than atoms?
I'm trying to calculate dipole moments from Wannier centers for the first time and there are basics I don't understand and can't figure out from online resources.
The software I'm using has a simple &...
12
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1answer
153 views
Creating Interatomic Potential for Lammps using DFT
What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
7
votes
1answer
107 views
How do I build and run a simulation of water molecules in NAMD?
So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
4
votes
1answer
76 views
Simulating polymers using cellular automata?
I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
9
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0answers
83 views
Is "Valence Electron Density" and "Electron Density" data of a molecule the same thing? [closed]
I'm wondering specifically in the context of calculating physical properties from valence-electron-density data using DFT, MD, and or ML (machine learning).
8
votes
1answer
134 views
How to address the errors on Automated Topology Builder?
I was trying to get the charges and the topology file for this molecule ($\ce{C28H58O7S8}$).
But I get the following error despite using the right number of hydrogens.
...
12
votes
1answer
62 views
What does this temperature & total free energy profile mean (obtained from VASP NVT molecular dynamics simulations)?
In order to obtain molecular dynamics (MD) simulations trajectory for computing phonon dispersion relation at finite temperature, I performed NVT MD simulation using VASP for my target system.
Here is ...
6
votes
1answer
44 views
Can we assume that the intraceullular pH and intermembrane pH are the same when calculating the protonation state of a protein subunit?
I want to know the protonation state of the intermembrane subunit of a protein.
For that, I need to know the pH, so given that small molecules can cross the lipid bilayer, could we assume ...
15
votes
6answers
2k views
How do I simulate the interaction between two atoms?
I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
7
votes
1answer
55 views
How to calculate the volumetric energy density of a molecule?
I am trying to store hydrogen in a hydrocarbon.
The example can be taken as cyclohexane ($\ce{C6H12}$) which is in a hydrogen-rich state. Its hydrogen-lean state is Benzene.
I want to calculate the ...
7
votes
1answer
58 views
How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?
When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
3
votes
1answer
38 views
Missing residues in ATB downloaded pdb/rtp files
I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md)
Two files are available: a PDB file and a topology ITP/RTP file.
The name of the ...
11
votes
2answers
62 views
What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?
I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
8
votes
2answers
217 views
Large pressure fluctuations in molecular dynamics
I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level.
For example, I set the pressure at 1 bar and it averages ...
13
votes
1answer
150 views
Minimum image convention for non-orthorhombic unit cells
I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells.
I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...