A tool to export common trajectory file from Materials Studio

Features

• Support full periodic boundary conditions

  Please note that this tool has converted the coordinates to match the PDB unit cell and coordinates exported by MS, so there may be differences from the original data output by Perl/Trj2Ascii, especially for the triclinic system.

• Support export move + fix atoms if exist .pdb

• Support export xyz trajectory file

• Support export xtc of gromacs file (includes time and step)

• Support export .trr format which contains velocities (nm/ps) and forces(kJ/mol/nm) if it exists

  Note that fixed atoms will have zero velocity and force, meaning their coordinates/velocity/force data won't appear in the .trj file.

• Support export .txt format (Plain text file) which contains all kinds of energy items and others:

  #Time(ps) Temperature(K) Potential(kJ/mol) Kinetic(KJ/mol) TotalEnergy(KJ/mol) Pressure(bar) Volume(A^3)
  

• Support .whl for Python API

  pip install xxx.whl
  

  Usage reference: api_test

Usage

First locate molecular dynamics trajectory file created by Materials Studio, hidden file .trj and .xtd are located in same folder.

Then download program from here: Download

• Linux

  chmod a+x MS_dump
  ./MS_dump -s system.pdb -f system.trj
  

• Windows

  .\MS_dump.exe -s system.pdb -f system.trj
  

Default output MS_traj.xyz, the comment line has box information that can be read by Ovito software directly.

Lattice="14.408798 0.0 0.0 0.000000 14.408798 0.0 0.000000 0.000000 14.408798" Properties=species:S:1:pos:R:3

Note:

The exported xyz will use C name for all atoms if not provide pdb file, such as:

.\MS_dump.exe -f system.trj

-o option can control output format

If you want to export .xtc/.trr of gromacs, use command:

.\MS_dump.exe -s system.pdb -f system.trj -o system.xtc

.\MS_dump.exe -s system.pdb -f system.trj -o system.trr

Also export energy items:

.\MS_dump.exe -f system.trj -o energy.txt