Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
82
questions
9
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1answer
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Is there a way to understand pi-pi interactions through GROMACS?
I have two polymer molecules with benzene rings as a part of them. I would like to understand how the interactions between them influences the solvability of the polymer in a non-aqeous solvent. I ...
7
votes
0answers
25 views
Reaction simulation at specific temperature, pH and pressure
Can we design metal organic framework, layered double hydroxide using LAMMPS? How?
8
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1answer
53 views
Generating topology for charged molecules
I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
8
votes
0answers
58 views
Why does my calculation using GROMACS get stuck at step 0?
I have been using the HPCE on our campus for MD simulations using GROMACS.
However, when I use the following script, after the job starts to run on the cluster, gets stuck at Step 0 in the log file.
<...
8
votes
1answer
45 views
What is the state-of-the-art in current flexible water models?
Do we have water models so far which are flexible? How good can they model specific properties of water and are they currently used with force fields and in actual simulations?
6
votes
1answer
42 views
Is it possible to simulate the Raman spectra via Molecular Dynamics (MD) using the GROMACS package?
I'm new to molecular dynamics and DFT. The aim was to study the Raman spectra of a molecule in a medium. As we know the Raman spectra of a molecule change due to the induced polarization in the ...
9
votes
1answer
132 views
Computational biology textbook similar to “Computational Materials Science” by June Gunn Lee
I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee.
In his book, Lee discusses the theory of MD ...
10
votes
2answers
67 views
Choosing RAM, CPU time, # of cores, and other parameters for an MD run
I did an AIMD run in VASP using 64 cores (32 cores/node) and 250 GB of memory (125 GB/node) for 5 ps (1 fs time step). The calculation took 12.6 hours to complete. CPU efficiency was 99.7% and memory ...
14
votes
1answer
62 views
How exactly does one compute the vibrational density of states from the output of a molecular dynamics simulation?
There are many things that can be done with the output of a molecular dynamics simulation, but one of the more powerful things is the ability to compute the vibrational density of states (or the ...
11
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0answers
69 views
Empirically determining thermostat damping factor
tl;dr Is there a way to determine an appropriate thermostat damping factor given a timestep size and a numerical integration method?
I am computing a set of simulations in LAMMPS, using ReaxFF, ...
18
votes
2answers
698 views
Why do people care about reversibility in molecular dynamics simulations?
When carrying out a molecular dynamics simulation, one has to choose an ensemble. Depending on the problem, one usually works in the microcanonical (NVE), canonical (NVT), or grand canonical ensemble (...
6
votes
1answer
60 views
Software recommendations for peptide conformation
I have a series of alanine dipeptide trajectories and would like to get the conformation type ($\alpha$, $\beta$, etc.) from the atom coordinates or dihedral angles. Does any package (like RDKit for ...
8
votes
1answer
51 views
Finding conformations of peptide based on dihedral angles
I was trying to look at the alanine dipeptide trajectories from this link and track the trajectories in a Ramachandran plot. Below is a plot based on dihedral angles at each timestep for all ...
14
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0answers
42 views
Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields
Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
6
votes
1answer
54 views
Dihedral angles of alanine dipeptide
I have a number of trajectories of alanine dipeptide molecule and I'm interested in computing dihedral angles of each configuration.
$\quad\quad\quad\quad$
Have I selected the right atoms for ...
8
votes
0answers
59 views
Equilibration of normal modes in water molecule [closed]
When running a molecular dynamics simulation on a singular water molecule in vacuum to analyze its normal modes of vibration from the NVE (microcanonical) ensemble, the bending mode frequency is ...
8
votes
2answers
67 views
Tools for structural analysis on LAMMPS trajectories
I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
9
votes
2answers
48 views
Evaluating the MSD of my simulation
I am running a molecular dynamics simulation of water in TIP3P, and I am storing the positions of my particles in a 2D array called relevant_positions. The number ...
9
votes
1answer
93 views
How does one compute the boiling point of a liquid made of a particular molecule?
This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE.
I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
8
votes
1answer
108 views
How to calculate the orthogonal representation of a HCP cell?
I'm trying to write a program to calculate the neighbor lists of crystal systems. I found a few codes that are able to calculate it for orthogonal systems. How can I do it for non-orthogonal cells ?
...
7
votes
1answer
71 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 ...
9
votes
1answer
84 views
AIMD and velocity scaling in VASP
Typically one does velocity scaling to "heat" their sample with MD.
How do we do this in VASP? Is it by setting the SMASS=-1 and ...
8
votes
2answers
79 views
Alanine dipeptide trajectories dataset
I was looking for a dataset of alanine dipeptide trajectories. I was wondering whether there is such dataset available or it is unlikely to find one and I should start running molecular dynamics ...
9
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2answers
113 views
How to build a simulation model for a molecular dynamics simulation
I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
8
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0answers
53 views
How much of a difference in a protein's radius of gyration can be considered significant?
In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein.
When comparing two protein radius of gyration, what difference can be ...
8
votes
1answer
89 views
Modelling water using the TIP3P flexible system [closed]
I am modelling water using a TIP3P flexible system. I am using the pair, bond and angle parameters given on the LAMMPS webpage. I am trying to run an $NPT$ simulation at $298\,K$ and $1 \,\mathrm{atm}$...
15
votes
1answer
128 views
Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?
I would be very grateful for some newbie-level advice from a thermodynamics guru.
I ran NPT simulations on a particular system (in CP2K software) to get fluid densities for use in fluid dynamics ...
7
votes
0answers
57 views
Collective variable to determine the number of bonds in the shortest Hydrogen bond wire
I am trying to program a collective variable in PLUMED which is basically the number of bonds in the shortest Hydrogen bond wire in a system of water molecules. I plan to use the HBond_Matrix from ...
8
votes
1answer
69 views
Using the VACF command in LAMMPS to get the velocity autocorrelation function
I am writing a simple Lennard-Jones fluid simulation in LAMMPS.
So far, I have outputted the temperature, volume, density, total energy, enthalpy, pressure, and all of it seems to be believable every ...
7
votes
0answers
91 views
How to do molecular dynamics calculations and analyse trajectories of small molecules? [closed]
I need to perform some MD calculations and then trajectories of some small molecules analyzed.
What I have is
protein
cofactor (FAD)
small molecule (either single O2 molecule or single Chlorine atom)
...
9
votes
1answer
136 views
Can I compute the free energy difference in (temporally) nearby micro-states using the Zwanzig equation for Free Energy Perturbation?
I wanted to understand the Free Energy Perturbation in an NVT ensemble.
Wikipedia explains it as:
$$
\tag{1}
\Delta F = F_1 - F_0 = -\kappa T \ln \left<\exp\left( \frac{-(E_1-E_0)}{\kappa T}\right)...
19
votes
2answers
654 views
Does increasing Lennard-Jones cutoff means higher accuracy?
I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
11
votes
1answer
86 views
Modelling Diffusion of Molecules Through a Physical Barrier
I would like to model the diffusion of various small molecules (e.g. $\ce{O2}$, $\ce{H2O}$, $\ce{MeOH}$, etc.) through polymeric barrier material (e.g. polyethylene, ethylene vinyl alcohol, ...
7
votes
1answer
120 views
Does the Hamiltonian of an unbiased simulation change when the simulation moves from a stable basin to another?
I wanted to understand the change in the Hamiltonian function as an unbiased simulation goes from one stable basin to the other.
Does the Hamiltonian stay constant or does it change as the unbiased ...
16
votes
3answers
435 views
References for Molecular Dynamics?
I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
8
votes
1answer
100 views
What is the “overcoherence problem” in Ehrenfest dynamics?
I am a novice in Ehrenfest dynamics and would like to know why Ehrenfest dynamics suffers from the "overcoherence problem"?
5
votes
0answers
47 views
What is the difference between Ehrenfest dynamics and Born-Oppenheimer Molecular Dynamics? [duplicate]
What is the fundamental difference(s) between Ehrenfest dynamics and Born-Oppenheimer MD? Also, in what situation(s) or case(s) one is preferred than the other one?
11
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0answers
70 views
Calculate free energy for a canonical (NVT) ensemble [closed]
I have an NVT ensemble of water molecules (liquid) and I want to calculate the Free energy (helmholtz or gibbs) whichever is equivalent to the following relation:
$$ \Delta F = -RTlnQ $$
I can't ...
10
votes
2answers
234 views
What are the factors to consider before docking 2 proteins?
With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
10
votes
0answers
51 views
Setting multiple new atype/dtype/itype with LAMMPS fix bond/create
When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
10
votes
1answer
58 views
What does the Neighbor command do in LAMMPS?
I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
5
votes
1answer
64 views
Why am I losing bonds when I use PACKMOL on two proteins?
I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code:
...
11
votes
1answer
67 views
LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands
I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
7
votes
1answer
82 views
What are the types of Quantum Molecular Dynamics (QMD)?
In similar spirit to recent questions on Quantum Monte Carlo, ab-initio Molecular Dynamics, types of SCF, and others, I would like to ask:
What are the types of Quantum Molecular Dynamics (QMD)?
As I ...
10
votes
0answers
53 views
Sample LAMMPS file for graphene growth on a metal surface
I am working with graphene growth on metal substrates. But I need some sample codes to know if I am doing it in the right way because running multiple simulations in LAMMPS takes a lot of time. Can ...
10
votes
1answer
95 views
How can I calculate the Poisson ratio of an amorphous material with LAMMPS?
I noticed that we can calculate the Poisson ratio of a crystalline metals with LAMMPS. I wonder if we can use that example for a metallic glass! If no, is there any other way, with another software?
11
votes
1answer
110 views
Dealing with symmetry of ordered primitive cell during DFT structure relaxation
I have a large disordered cubic structure that I would like to do AIMD on to look at cation diffusion. I found the primitive cell and then ordered it to create several configurations. I will then ...
9
votes
0answers
69 views
I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]
I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python.
I have written a ...
11
votes
2answers
88 views
Calculating diffusion coefficient from Mean Squared Displacement
I am performing a molecular dynamics simulation and I have calculated the velocity autocorrelation function (VACF), $\psi (t)$ and mean square displacement, $\langle (\Delta r)^2 \rangle$. In my ...
10
votes
2answers
171 views
What are some methods for modeling bulk phase infrared spectra?
I am interested in predicting the infrared spectra of bulk phase molecules, it seems that AIMD (ab initio molecular dynamics) is the current best approach. I have found a tutorial on using CP2K to do ...
