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
xyztrajectory file -
Support export
xtcof gromacs file (includes time and step) -
Support export
.trrformat which contains velocities (nm/ps) and forces(kJ/mol/nm)if it existsNote that fixed atoms will have zero velocity and force, meaning their coordinates/velocity/force data won't appear in the
.trjfile. -
Support export
.txtformat (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 Python API
pip install PyMSDumpUsage 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
Cname 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
Release files for PyMSDump 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| pymsdump-0.1.1-cp314-cp314-win_amd64.whl | CPython 3.14 | CPython 3.14 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.14 | CPython 3.14 | Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| pymsdump-0.1.1-cp313-cp313-win_amd64.whl | CPython 3.13 | CPython 3.13 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.13 | CPython 3.13 | Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| pymsdump-0.1.1-cp312-cp312-win_amd64.whl | CPython 3.12 | CPython 3.12 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| pymsdump-0.1.1-cp311-cp311-win_amd64.whl | CPython 3.11 | CPython 3.11 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| pymsdump-0.1.1-cp310-cp310-win_amd64.whl | CPython 3.10 | CPython 3.10 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.10 | CPython 3.10 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| pymsdump-0.1.1-cp39-cp39-win_amd64.whl | CPython 3.9 | CPython 3.9 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
| pymsdump-0.1.1-cp38-cp38-win_amd64.whl | CPython 3.8 | CPython 3.8 | Windows x86-64 | Details |
| pymsdump-0.1.1-cp38-cp38-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 | Details |
Total release size: 2.0 MB
Release files / pymsdump-0.1.1-cp314-cp314-win_amd64.whl
| Download URL | pymsdump-0.1.1-cp314-cp314-win_amd64.whl |
|---|---|
| Size | 134.6 kB |
| Tags | CPython 3.14 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
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| Download URL | pymsdump-0.1.1-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
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| Size | 161.5 kB |
| Tags | CPython 3.14 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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| Download URL | pymsdump-0.1.1-cp313-cp313-win_amd64.whl |
|---|---|
| Size | 130.7 kB |
| Tags | CPython 3.13 Windows x86-64 |
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| Download URL | pymsdump-0.1.1-cp312-cp312-win_amd64.whl |
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| Tags | CPython 3.12 Windows x86-64 |
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| Tags | CPython 3.12 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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| Tags | CPython 3.11 Windows x86-64 |
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| Download URL | pymsdump-0.1.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
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| Size | 158.1 kB |
| Tags | CPython 3.11 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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| Tags | CPython 3.10 Windows x86-64 |
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| Size | 156.5 kB |
| Tags | CPython 3.10 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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| Size | 130.9 kB |
| Tags | CPython 3.9 Windows x86-64 |
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| Tags | CPython 3.9 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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| Tags | CPython 3.8 Windows x86-64 |
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| Tags | CPython 3.8 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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