# Materials-Studio-script

**Repository Path**: raow/Materials-Studio-script

## Basic Information

- **Project Name**: Materials-Studio-script
- **Description**: perl script of Materials Studio
- **Primary Language**: Perl
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 12
- **Forks**: 6
- **Created**: 2020-05-25
- **Last Updated**: 2024-02-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: ms, md, 扩散, 吸附, 化学反应

## README

# Materials-Studio-script
All scripts can be run in the Materials Studio, involving Monte Carlo, Molecular Dynamics.
All scripts can be executed on server, in order to free your PC

**If you have any questions about the perl script in the Materials Studio, you can contact me via email: weirao100@qq.com**

## All.pl
Including the coordinates and dipolemoment of atoms, MSD, concentration of the molecules in the set of trajectory, Potential Energy component, Radial Distribution Function and Radius Of Gyration.

## CenterInBox.pl
Export the coordiantes of molecular center every frames from the trajectory, which must be within one periodic box.

The initial coordiantes of every atom may be out of the periodic box, and then the final coordinate are put in the box after running this script.

## Config.pl
Alkane diffuses in the channel of zeolite, recorded in the **MOR-C12.xsd**, now we need execute the *dlpoly*, a molecular dynamics package, rather than the *Materilas studio*. The input file of *dlpoly*, named as CONFIG, can be transferred via the **MOR-C12.xsd** by this perl script. It is worthing noting that the force field of this task is taken from the [ref 1](https://pubs.acs.org/doi/10.1021/ct900315r) and [ref 2](https://pubs.acs.org/doi/10.1021/ja0476056).


## EnergyExtract.pl
Extract the all kinds of energy data from *std* file.

## fractionalX.pl
obtain the atmoic fractional coordiantes from *.cif file


## InZeo.pl
molecules may be in zeolite or the vacuumn,, thus this script can be used to determine the number of molecules in zeolite every frames from trajectory file

## MS.sh
Commit computational job to qsub. In MS.sh, you can rewrite cores of CPU, name of jobs, etc. There is one thing to be noted that you must change location of  *RunMatScript.sh*


## Stress.pl
Create set including molecules and Calculate StressAutocorrelationFunction

## Transfer.pl
Transfer a cif file to be xyz and pdb or a new cif file and then output the lattice information.


## xsd\_qsub.sh
Carry out the command, *qsub MS.sh*


## xxx.bat
show the diffusion trajectory via cartoon using the VMD