# Molecular dynamics calculations

### This page gives hints on how to perform a molecular dynamics calculation with the ABINIT package.

##### Copyright (C) 2016-2017 ABINIT group (GG)

Mentioned in topic_GeoConstraints, help_features#4.

### Table of content:

- 1. Introduction.
- 2. Related lesson(s) of the tutorial.
- 3. Related input variables.
- 4. Selected input files.

### 1. Introduction.

Three molecular dynamics algorithm (Numerov, Verlet, Blanes and Moanes) allow to perform simulations in real (simulated) time, see ionmov. The displacement of atoms may be computed according to Newton's law, or by adding a friction force to it. Nose-Hoover thermostat is available with Verlet algorithm. Langevin dynamics is also available.

Specified lattice parameters, or angles, or atomic positions, can be kept fixed if needed, see topic_GeoConstraints.

The trajectories can be analyzed thanks to the APPA postprocessor.
Go to the top

### 2. Related lesson(s) of the tutorial.

- Parallelism for molecular dynamics calculations
Go to the top

### 3. Related input variables.

Compulsory input variables:

... dtion [Delta Time for IONs]
... ionmov [IONic MOVEs]
... mdtemp [Molecular Dynamics TEMPeratures]

Basic input variables:

... nnos [Number of NOSe masses]
... ntime [Number of TIME steps]
... qmass [Q thermostat MASS]
... vel [VELocity]
... vis [VIScosity]

Useful input variables:

... friction [internal FRICTION coefficient]
... nctime [NetCdf TIME between output of molecular dynamics informations]
... noseinert [NOSE thermostat INERTia factor]
... restartxf [RESTART from (X,F) history]

Input variables for experts:

... bmass [Barostat MASS]
... delayperm [DELAY between trials to PERMUTE atoms]
... densfor_pred [DENSity and FORces PREDictor]
... diismemory [Direct Inversion in the Iterative Subspace MEMORY]
... extrapwf [flag - EXTRAPolation of the Wave-Functions]
... mdwall [Molecular Dynamics WALL location]
... signperm [SIGN of PERMutation potential]
Go to the top

### 4. Selected input files.

WARNING : as of ABINITv8.6.x, the list of input files provided in the specific section of the topics Web pages is still to be reviewed/tuned. In some cases, it will be adequate, and in other cases, it might be incomplete, or perhaps even useless.
The user can find some related example input files in the ABINIT package in the directory /tests, or on the Web:

tests/mpiio/Input: t21.in t22.in

tests/fast/Input: t21.in t29.in

tests/paral/Input: t21.in t22.in t23.in

tests/v2/Input: t88.in

tests/v3/Input: t40.in

tests/v5/Input: t01.in t03.in t04.in

tests/v8/Input: t12.in
Go to the top