Questions tagged [molecular-dynamics]

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

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6
votes
1answer
33 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 ...
4
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0answers
29 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
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1answer
29 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
59 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
73 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
142 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 ...
4
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0answers
28 views

What will be the cohesive energy of an alloy in LAMMPS?

The cohesive energy of a pure material is generally termed as the energy of a unit cell divided by the number of atoms. what will be cohesive energy of an alloy in LAMMPS? I am running LAMMPS for $\ce{...
12
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1answer
144 views

Analyzing MD trajectory: molecule orientation

I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field. There are two order parameters that are used to ...
4
votes
1answer
43 views

Calculating Velocity autocorrelation function for Binary Diffusion Coefficient

I have been attempting for some time to evaluate the binary Diffusion coefficient of argon in a gas mixture with neon. From the literature, this property can be measured using the velocity ...
10
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1answer
76 views

How do I calculate the radial distribution function from the centre of mass of unit cell in GROMACS?

I am simulating a droplet of water with GROMACS. The droplet consists of about 200 TIP3P water molecules and is placed near the center of a large, mostly empty box (...
6
votes
1answer
58 views

Molecular dynamics: how to pack system for desired density

I'm trying to perform ab-initio MD on polymer system. I've built single chain of polycarbonate (PC) with the length of ~40 angstroms and now I'm building initial configuration. I've calculated how ...
8
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0answers
40 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 ...
6
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0answers
35 views

How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?

I am trying to reproduce the 2D SAXS interference pattern of bulk water via ab-initio MD methods as shown in the figure below: The main aim is to recreate figure (a) via averaging MD configurations ...
12
votes
1answer
85 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm. I first load a default system of particles (alanine-dipeptide in ...
7
votes
1answer
69 views

Using LAMMPS for a small system

I want to run a classical molecular dynamics simulation on silicane using LAMMPS. Since I don't have access to any HPC nor do I have a powerful desktop PC, I'm planning on making the system small. By ...
5
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1answer
37 views

Bulding host-guest polymer system for molecular dynamics

I'm thinking of running MD simulation of poling process (heating and cooling in external electric field) of host-guest polymer system: organic chromophore in polymer matrix (PMMA or polycarbonate). So,...
11
votes
1answer
71 views

Unable to recreate data for benzene from paper in GROMACS 2020.5

I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
10
votes
1answer
140 views

What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
7
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1answer
99 views

Molecular Dynamics Simulations in VASP

I want to run molecular dynamics (MD) simulations with VASP for Mg2Si to investigate the simulation time vs ENCUT and KPOINTS, ...
3
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0answers
65 views

Error in GROMACS for adding ions to a solution

I am following Justin Lemkul's GROMACS simulation given on this website here for GROMACS. I believe I have followed the process to the T. I would like to mention that in the "Generate Topology&...
9
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2answers
435 views

Is the dynamics of a peptide molecule Markovian?

I was wondering if the underlying dynamics of a full atomistic trajectory of a peptide molecule are Markovian. Note added after the first two answers: I assumed that they were Markovian, as they are ...
9
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2answers
92 views

Starting configuration for a molecular simulation

When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results? The book Computer Simulation of Liquids suggests putting the molecules on an ...
11
votes
3answers
385 views

Which ensemble to use for a molecular dynamics simulation?

Does it matter which ensemble you use for a molecular dynamics simulation? Shouldn't they in principle give the same results? Why, historically, was it hard (and desirable) to develop simulations in ...
9
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0answers
65 views

Selection of appropriate Langevin damping parameter for MD of solid metal

I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this. I have previously used the ...
8
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0answers
28 views

Lone pairs in CHARMM for molecular dynamics

I have a substrate that has a Br-C bond. In CHARRM the line below is included in the .str file: ...
7
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1answer
84 views

cp2k conserved quantity changed when restart NVT MD?

The details are descripted elsewhere, but got no answer for days, so I post it here for help. As title said, I noticed a relatively big change in conserved quantity and don't know why. I've upload ...
12
votes
1answer
248 views

Compute RDF between COMs of two selections (or groups) using GROMACS

I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...
12
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0answers
73 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
10
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0answers
67 views

Using Molecular Dynamics as an experimentalist to study how much plastic work is converted to heat, does anyone have any comments on our paper?

When you load a metal and the deformation results in permanent plastic deformation, the input work should be converted into heat and thus dissipate. But for about 100 years people have struggled to ...
13
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1answer
157 views

Visualizing MD generated electron density cubes as trajectories

During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
8
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0answers
55 views

Periodic polarizable QM/MM embedding

Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
6
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0answers
61 views

How to effectively simulate high density systems in GROMACS?

I have a system with a dense liquid solvent and a polymer solute. I have inserted all the molecules randomly using gmx insert-molecules and then did the energy minimization and equilibration steps to ...
9
votes
1answer
59 views

Algorithmic description of implementing path integral molecular dynamics?

Suppose I have a functioning molecular dynamics package for classical MD. I want to extend this code to run path integral MD. I know that a surprisingly small number of new features need to be ...
8
votes
1answer
113 views

Are there other kinds of stability of materials? How to demonstrate that with computation approaches?

I have known some kinds of stability of materials, such as: Mechanical stability; Dynamical stability; Thermal stability In particular, they can be studied with first-principles computational ...
7
votes
1answer
70 views

For ergodicity, what is the significance of the R value and slope?

I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to ...
6
votes
0answers
77 views

How to build amorphous Al2O3 using the AIMD method implemented in VASP?

I want to build amorphous Al$_2$O$_3$ with the AIMD (ab-initio molecular dynamics) method implemented in VASP. I know that two procedures should be taken into account, namely 1st: melt 2nd: quench ...
6
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0answers
33 views

How can I quantify the uncertainty of thermal molecule properties in molecular dynamics simulations?

When doing molecular dynamics simulations, there are countless sources of error (i.e. approximations and numerics). Molecular dynamics can be used to determine intrinsic thermal properties such as ...
9
votes
1answer
80 views

Methods to handle non-ergodic systems with Molecular Dynamics

Given the large difference between simulation timescales and the timescales on which we normally interact with ensembles of molecules, the time average of a molecular dynamics simulation does not ...
13
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2answers
336 views

Classical Monte Carlo vs. Molecular Dynamics

Both Classical Monte Carlo (MC) and Classical Molecular Dynamics (MD) simulations are used to perform simulations of ensembles of molecules. These MC calculations are calculating thermodynamic ...
6
votes
1answer
85 views

Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?

I'm looking for a simulation of different water models (TIP3P, SPC/E, TIP4P, water models with flexible bounds) where the differences in simulation speeds on a common architecture are really seen. ...
9
votes
1answer
81 views

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
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0answers
39 views

Reaction simulation at specific temperature, pH and pressure [closed]

Can we design metal organic frameworks, layered double hydroxide using LAMMPS? How? I want to synthesize a metal organic framework or such materials, and I want to ask if I put two to three chemicals ...
8
votes
1answer
54 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 ...
9
votes
1answer
199 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
57 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
99 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
142 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
79 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
131 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 ...
13
votes
0answers
108 views

Empirically determining thermostat damping factor

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, tracking ...