Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
401
questions
1
vote
0
answers
9
views
Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics
Can we calculate the absorption enthalpy at different temperature in VASP software via ab initio molecular dynamics? If yes, how?
- 33.5k
1
vote
0
answers
29
views
Free energy calculations for lammps
Is there any tutorial or reference available to perform free enegy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; widom's particle insertion method) etc. With ...
- 33.5k
3
votes
0
answers
19
views
How to perform atomistic spin dynamics (ASD) Ab Initio Molecular Dynamics (AIMD) using VASP?
I have tried normal AIMD simulation using VASP for Non magnetic materials. Now, I am interested to perform the molecular dynamics simulations for the finite temperature for Magnetic materials to ...
- 33.5k
3
votes
0
answers
20
views
How to get energy gap change at specific high symmetry points during ab initio molecular simulations？
I want to check the energy gap change during finite temperature ab initio molecular simulations. The results may look like this picture:
How can set aimd simulation to get this result in VASP?
- 405
3
votes
0
answers
96
views
Include Li+ in force field for Molecular Dynamics
I want to perform some MD including Li+ ions. Specifically I am interested in Li-TFSI (aka Lithium bis(trifluoromethanesulfonyl)imide).
I tested both the ATB repository and LigParGen and neither can ...
- 667
1
vote
0
answers
18
views
When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
- 11
8
votes
2
answers
121
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 ...
- 2,628
3
votes
1
answer
43
views
Adsorption of Li on GeC (optimization problem)
Actually I am trying to study the adsorption of Li or K on the sheet starting from the hexagon centre the system optimises with Li or (K) adsorbed over one of the Ge atoms and not remain at the centre....
- 695
3
votes
0
answers
43
views
Read and run lammps water model in ASE
I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly.
ASE is not able to read the <...
- 2,885
1
vote
0
answers
11
views
What are the appropriate boundary conditions for simulating shear deformation of a screw dislocation in LAMMPS?
I'm seeking clarification on the selection of suitable boundary conditions for simulating shear deformation of a screw dislocation using LAMMPS. In my script, I currently employ the following commands:...
- 11
1
vote
0
answers
52
views
Issue building deepmd kit for a plugin version of LAMMPS
I am following the deepmd-kit documentation to implement this kit into a plugin version of LAMMPS, the documentation I am using is found here and here. I am close to completing everything, but am ...
- 43
2
votes
0
answers
58
views
Simulate liquid solvent mobility through a gel polymer electrolyte
I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such a system?
Three ...
- 667
3
votes
1
answer
86
views
NPT Molecular dynamics calculation problem
I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem?
This is my code for the heating part. However, the ...
- 33.5k
3
votes
1
answer
49
views
What is a 'mover' in molecular dynamics?
Movers
What is a 'mover' in molecular dynamics?
Can you supply me with reading material on 'mover'?
- 33.5k
4
votes
0
answers
33
views
How to extract Lindemann Index from LAMMPS dump files?
I used a python code to extract Lindemann index from dump files. But the problem is the code works fine with dump files with little amount of data and atoms. When I use large files if shows overflow ...
- 1,579
5
votes
2
answers
150
views
How is the equation for the position of a virtual site derived?
Cross posted on Math SE
I am trying to understand virtual sites in MD simulations, and I came across this configuration:
Here, coordinate $\mathbf{s}$ represents the virtual site, which is formed by ...
- 15.2k
3
votes
2
answers
98
views
Adsorption of naphthalene on graphene oxide sheets with gmx
How to set up a molecular dynamics (MD) simulation for the adsorption of naphthalene on graphene oxide sheets using GROMACS?
- 1,031
4
votes
0
answers
59
views
ASE/XTB: zero temperature and stress in MD simulation
I want to see how the volume and pressure of my cell is changing during a MD relaxation in ASE. I used the atom.get_volume() and ...
- 667
4
votes
1
answer
148
views
ASE: Shape mismatch when using FrechetCellFilter filter
I want to use a FrechetCellFilter into a MD simulation with ASE to make sure both the atomic forces and unit cell are simultaneously minimised.
I encounter a ...
- 667
9
votes
2
answers
133
views
Berendsen thermostat: why are the two time constants not equal?
With reference to the GROMACS manual 2023.2, the discussion of the Berendsen thermostat (p. 362) indicates that the time constant $\tau$ which governs the steepness of the relaxation toward a target ...
- 2,628
3
votes
0
answers
36
views
Running molecular docking simulation between two proteins
i did run docking simulation between two proteins on HADDOCK server
but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it
best ...
- 31
8
votes
0
answers
83
views
How to go from zero to hero in Machine Learning for materials modelling
I am interested in exploring the use of machine learning tools to accelerate molecular dynamics simulation probably by training machine learning potentials. While I have found some papers that apply ...
- 443
3
votes
0
answers
62
views
I need molecular dynamics simulations input file for hexagonal heterostructures in quantum espresso [closed]
I m a material science student of PhD and search alot and make some input files for AIMD simulation but I didn't get the best output if anyone have the input file please provide me
- 33.5k
3
votes
1
answer
109
views
Finding the total energy using quantum espresso
I am a beginner in Quantum Espresso
When I want to calculate the total energy for Cu for example, I write the input file for primitive cell or conventional cell, what is the difference?
Thank you
- 6,567
16
votes
2
answers
827
views
How may I create an interatomic potential using DFT?
What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
- 81
2
votes
0
answers
55
views
Method for Energy Computation of Protein Structures
So far i have found only one paper that describes how we can compute protein energy while doing MD simulation:
Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...
- 33.5k
-5
votes
1
answer
92
views
Are these simulator, visualizer, or force field? [closed]
I see that some "names" are available online in relation to MD simulation.
VMD
NAMD
LAMMPS
OpenMM
GROMACS
Amber
CHARMM
Are these "names" simulators, visualizers, force fields, or ...
- 2,352
4
votes
1
answer
349
views
Which MD software is preferable for protein simulation?
I see that some free MD simulation software are available online.
VMD
NAMD
LAMMPS
OpenMM
GROMACS
Amber
CHARMM
Which one above is the most appropriate for protein simulation?
- 890
4
votes
0
answers
39
views
OOM Error Calculating ESP Charges with Psi4
I'm trying to create a script to generate partial charges for a given .dat file.
As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro ...
- 33.5k
3
votes
1
answer
228
views
"ERROR: Lost atoms" while simulating N2/CO2 mixture
I am trying to simulate a mixture of CO2 and N2 but I keep getting ERROR: lost atoms: original 1500 current 1495. I have performed several energy minimizations and ...
- 15.2k
2
votes
0
answers
72
views
Help with LAMMPS create_atoms and delete_atoms command
I am running polymer simulations inside a spherical region. I have loaded the polymer using read_data command. I want to add fixed number of individual new atom types inside this sphere while it ...
- 453
12
votes
2
answers
923
views
Algorithm for calculating dielectric constant of water TIP3P
I am running a NVT TIP3P simulation of water with 125 molecules of water in a 16-by-16-16 angstrom box with periodic boundary conditions on LAMMPS, with a time-step of 1 fs for 10 ps.
Once the ...
- 141
5
votes
2
answers
718
views
About neigh_modify and dangerous builds in LAMMPS
I am doing a simulation of a 3D LJ system in LAMMPS, where I am heating an already equilibrated configuration at $T^* = 0.3$ to $T^* = 0.4$ for $1000000$ steps then equilibrating the same at $T^* = 0....
- 156
4
votes
0
answers
38
views
MMGBSA: Electrostatic and van der Waals
I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
- 41
15
votes
1
answer
618
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 ...
- 1,883
1
vote
0
answers
54
views
Where should we compute `Energy` in this listing?
Cross-posted here.
I have the following listing for a barebone MD simulation:
...
- 33.5k
2
votes
0
answers
45
views
Where should we compute `Trajectory` in this listing?
Cross-posted here.
I have the following listing for a barebone MD simulation:
...
- 33.5k
3
votes
0
answers
96
views
How to check the units from ASE get_forces() function?
Here is a little python code that loops through a molecular dynamics trajectory (performed with the ASE package) and outputs the forces on the atoms at each frame:
...
- 2,885
4
votes
0
answers
44
views
Quantifying binding free energy?
I have binding free energy of some organic molecules on a surface, computed through Umbrella sampling. For now, I only have experimental data on the binding energy of some of these molecules. Is it ...
- 1,031
3
votes
1
answer
50
views
Is the following description talking about the simulation box or the boundary condition?
Is the following description talking about the simulation box or the boundary condition?
To prevent the argon atoms in the gas phase from running off to
infinity, we enclose the system in a "...
- 6,567
4
votes
0
answers
32
views
How to create a water droplet (half-sphere) on a rock (quartz) surface
I am to Equilibrate a uniformly distributed spc water molecules at 300k in 50x50x50 box. Water density is taken to be 1000kg/m3. Simulate the system in the NVT ensemble. The spc water is modeled using ...
10
votes
1
answer
364
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, ...
-4
votes
1
answer
301
views
How may I make a slab surface to calculate a thin layer with Quantum ESPRESSO?
I want to know how to calculate the band structure and DOS of a thin layer of iron selenide in quantum espresso. How I can fix the input file? Is it different from Bulk matter or the same? Which ...
- 15.2k
2
votes
0
answers
30
views
How to estimate the minimal distance between atoms for which a pseudopotential-based AIMD gets forces correctly?
I am doing ab initio molecular dynamics in VASP. As far as I know, pseudopotentials approximate all-electron potential far from the nucleus, and deviate from it near the nucleus.
When some of my atoms ...
5
votes
1
answer
757
views
Why are Coulomb interactions modeled with just r, not r squared?
As far as I understand (as a complete beginner to molecular simulation and modelling), Coulomb's law for two atoms i and j is:
$$F=k\frac{q_iq_j}{(r_{ij})^2}$$
(the force is proportional to the ...
- 15.2k
3
votes
2
answers
420
views
How to compute 2D density maps in GROMACS?
I have a GROMACS trajectory of MD simulation. I want to make a contour plot of density as a function of two coordinates, namely X and Z. Is it possible to get this using ...
- 121
3
votes
0
answers
47
views
Is it possible to find a cubic supercell for a non-cubic crystal structure?
Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
- 211
3
votes
0
answers
52
views
Are the Lagrange multipliers used in Kohn-Sham DFT/HF-based quantum molecular dynamics real valued?
I have seen it written in several places that the matrix of Lagrange multipliers used to impose orthonormality in quantum molecular dynamics schemes based on Kohn-Sham DFT or Hartree-Fock for instance,...
- 141
4
votes
1
answer
200
views
Contribution to pressure tensor from water
Cross-posted later on Reddit.
I have an infinite CG model of the material solvated in water. I am trying to apply a uniaxial deformation along a particular x-axis; the mdp settings in GROMACS are ...
CommunityBot
- 1
6
votes
2
answers
448
views
Effect of temperature on Forcefield parameters in classical molecular dynamics simulations
In classical molecular dynamics simulations of complex molecular systems, the force field (FF) contains information about bonded (bonds, angles, dihedrals and impropers) and non-bonded parameters. It ...
- 2,742