Questions tagged [molecular-dynamics]

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

15 questions with no upvoted or accepted answers
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13
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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 ...
9
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0answers
47 views

What kind of physical properties can be calculated from the “Valence Electron Density” data of a molecule?

I'm wondering specifically in the context of calculating physical properties from valence-electron-density data using DFT, MD, and or ML (machine learning).
9
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0answers
81 views

Is there any code that runs WHAM starting from histograms rather than time series?

I'm looking for a way to run the Weighted Histogram Analsys Method, but I don't have a time series to feed to the code as usually happens, but rather I have histograms coming from the debiasing of a ...
8
votes
0answers
30 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: ...
8
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0answers
56 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 ...
7
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0answers
29 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
0answers
70 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 ...
7
votes
0answers
107 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
votes
0answers
24 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 ...
6
votes
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 ...
6
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0answers
34 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 ...
5
votes
0answers
90 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
4
votes
0answers
18 views

Can we calculate the intermembrane protonation state?

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 intracelular ...
4
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0answers
33 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{...
3
votes
0answers
137 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&...