Questions tagged [molecular-dynamics]

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

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3 votes
0 answers
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I have a problem with Amber18 configuration at the make install step

I have a problem installing Amber. First, I enter the command: ./configure --with-python /usr/bin/python3 --with-netcdf $AMBERHOME/netCDF gnu Than make: ...
4 votes
1 answer
73 views

How to generate a polymer in different conformations?

I want to run MD simulations of a polymer, but I want to start from different physical conformations. My question is, how do I obtain these conformations? Is there a software which performs this? Let'...
2 votes
1 answer
25 views

How to control the thickness of lipid bilayer with GROMACS

I was trying to perform lipid bilayer MD for my protein based on GROMACS's Membrane Protein Tutorial. I can successfully orient the protein in the lipid (turquoise) as you can see in the image below: ...
6 votes
2 answers
78 views

Long Range Forces in Protein MD Simuation

I am trying to understand how long range forces are calculated under the following situation. SYSTEM-> Lets say we have a single protein surrounded by water molecules. Now I would like to run MD ...
3 votes
2 answers
36 views

How to orient the protein for lipid bilayer simulation in Gromacs

I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer. The domain of the protein looks like this: Thus I'd like to have the transmembrane part of the protein to be buried in lipid ...
5 votes
2 answers
272 views

How to apply FIRE to many atoms where P=F·v seems to be a vector rather than a scalar?

Introduction/Preamble @SusiLehtola's answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions conjugate gradients, BFGS for energy minimization, Metropolis ...
7 votes
2 answers
123 views

Which equation makes it possible to calculate the forces of attraction between a surface and molecules?

Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation? [Clarification 1] Between a ...
6 votes
1 answer
64 views

How to check for phase separation in polymer simulations?

Suppose I am running a molecular dynamics simulation of a polymer solution that exhibits upper critical solution temperature. From standard solution thermodynamics, we expect to see a polymer-rich ...
8 votes
0 answers
104 views

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 ...
2 votes
0 answers
16 views

Appropriate choice of force constant of spring to use for Steered molecular dynamics

As per Boltzmann distribution, the variance, or the fluctuation in length squared is given by $$\sigma^2 = \frac{k_BT}{k_{spring}}$$ Since $k_{spring}$ determines how strong the force I am applying to ...
2 votes
0 answers
43 views

Re-parametrization of force fields in LAMMPS

I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
3 votes
0 answers
25 views

Density of a spherical droplet of water on top of graphene

I produced a spherical droplet of water by having a box of water (sufficient water molecules inside the box to give the right density of water) on top of a 2d sheet-like graphene. The box becomes a ...
2 votes
0 answers
19 views

Measuring density as a function of two coordinates (namely X, and Y) in gromacs

I have a gromacs trajectory of MD simulation. Here, I want to make a contour plot of density as a function of two coordinates, namely X and Z. Is there anyway we can obtain such data with gmx density? ...
2 votes
1 answer
71 views

Is there a scripted tool to add neutral terminal caps (e.g. NME, ACE) to peptide chains for use with AMBER forcefields?

I have a range of systems consisting of multiple peptide chains, some of which are one residue (i.e. single amino acids), which I'd like to analyse using molecular dynamics and AMBER-flavour ...
3 votes
0 answers
31 views

How may I define the pressures of two sides of a membrane in Materials Studio? [closed]

To study 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: ...
13 votes
0 answers
321 views

How to calculate RDFs for MD trajectories without PBC, directly from coordinates?

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a program that could calculate the radial distribution function from ion to oxygen (or ion to ...
3 votes
0 answers
44 views

Lennard Jones Clusters in Python

I would like to explore the global optimisation of Lennard-Jones clusters in Python. I do not come from a physical chemistry background. I would like to be able to calculate the cluster energy ...
7 votes
1 answer
92 views

Water Dimer and Free Energy Perturbation (FEP)

I am trying to understand the FEP in the context of water dimer. Let's say I want to calculate $\Delta A$, the free energy change for the following reaction: $\ce{H_2O +H_2O\rightarrow H_2O-H_2O}$, ...
5 votes
1 answer
57 views

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'...
4 votes
1 answer
164 views

Scripts to calculate ionic diffusivity

I found several AIMD analyzers to estimate mean square displacement and ionic diffusivity such as pymatgen, mo, vaspkit. I tried some tests and found that the same data set might result in different ...
7 votes
1 answer
98 views

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 ...
7 votes
1 answer
148 views

Langevin vs Nosé–Hoover thermostat

can anyone explain the pros and cons of using the Langevin vs Nosé–Hoover thermostat? I wonder how to choose a suitable thermostat for a system, such as oxide, organic materials.
15 votes
2 answers
533 views

What are the parameters that need to be calculated to design the structure of a molecule?

Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
4 votes
1 answer
65 views

How to assign a "Boltzmann weight"?

I would like to assign a "Boltzmann weight" i.e. $\exp(-E/kT)$ to interactions between particles based on the relative energies. But wouldn't the largest particle-particle energies have the ...
2 votes
0 answers
45 views

Why is my pdb looking so weird?

I have generated the following pdb file for a polymer: ...
4 votes
0 answers
49 views

Simulated annealing of small protein

I understand the general concept of simulated annealing and have seen various criteria in papers, but I was wondering if there is a general rule of thumb for selecting a final structure, how many ...
19 votes
1 answer
962 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 ...
1 vote
1 answer
102 views

What does "dynamics" mean in matter modeling?

As an example, I have seen the phrase "dynamics of proteins" or "dynamics of biomolecules". The review paper "Protein Dynamics" by J A McCammon has the word in its title, ...
2 votes
0 answers
39 views

Martini 3 CG water cluster is not becoming spherical under NVT conditions

When we put a certain number of molecules in a small cubic box, and put it inside a large cubic box, under NVT simulation, the water cubic box is supposed to be spherical in shape to reach a minimum ...
3 votes
0 answers
43 views

Selecting the time lag and time window in calculating an MSD

A mean square displacement (MSD) can be calculated as either a time or an ensemble average. In the former, it is: $$msd(\tau)=<\Delta r(\tau)^{2}>=<[r(t+\tau)-r(t)]^{2}>$$ When calculating ...
6 votes
1 answer
125 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 ...
5 votes
1 answer
42 views

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 ...
3 votes
0 answers
39 views

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 ...
5 votes
0 answers
65 views

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....
4 votes
1 answer
24 views

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 ...
5 votes
2 answers
309 views

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, ...
7 votes
0 answers
136 views

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-...
16 votes
2 answers
729 views

Computing phonon dispersion from molecular dynamics simulations?

How would one obtain the phonon dispersion curve from a molecular dynamics simulation trajectory? What are the steps involved? Are there any packages that does this? If so, please mention them.
10 votes
1 answer
126 views

Understanding the rigorous bridge between atomistic and coarse-grained simulations

I am currently reading this paper by Noid et. al. on the rigorous bridge between atomistic and coarse-grained simulations. In the paper, he defined a linear map from the atomistic coordinates and ...
1 vote
1 answer
72 views

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)?
12 votes
2 answers
940 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 ...
4 votes
0 answers
122 views

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 ...
3 votes
0 answers
66 views

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?
4 votes
0 answers
39 views

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 ...
3 votes
0 answers
101 views

Calculating the Diffusion coffecients from Trajectory file in ASE [closed]

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 ...
4 votes
0 answers
141 views

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 ...
8 votes
1 answer
453 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 ...
3 votes
0 answers
50 views

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 ...
5 votes
1 answer
176 views

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 ...
4 votes
1 answer
363 views

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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