Added a list of abbreviations with meanings to the High Throughput Molecular Dynamics and Analysis Tutorials (Computational Chemistry) in response to feedbacks #2979
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…hput Molecular Dynamics and Analyses" (Computational Chemistry). issue galaxyproject#2978
Patch 1- Added abbreviations to the High Throughput Molecular Dynamics and Analysis Tutorials (Computational Chemistry) in response to feedbacks
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Thanks @Ezichi-Fav. |
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Hi @Ezichi-Fav, thanks a lot for the contribution! I wrote a few comments.
In general, I think it's important that the users understand what the abbreviations mean, not only what they stand for, so I suggested a few places where some more detail could be added. For example, to know what CHARMM stands for is not as important as to know what it actually is (a force field). :)
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| # Abbreviations | |||
| * **Hsp90** –Heat Shock Protein 90 <br> | |||
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| * **Hsp90** –Heat Shock Protein 90 <br> | |
| * **Hsp90** - Heat Shock Protein 90 |
Can you make sure you format the same on each line? With 1 space before and after the dash.
Also, the <br> tag should not be needed.
| * **MD**- Molecular Dynamics Simulation<br> | ||
| * **PDB**- Protein Data Bank<br> | ||
| * **GROMACS**- Groningen Machine for Chemical Simulation. It is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. <br> | ||
| * **GRO files**- GROMAC Format<br> |
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| * **GRO files**- GROMAC Format<br> | |
| * **GRO files**- structure file in GROMACS format |
| * **PDB**- Protein Data Bank<br> | ||
| * **GROMACS**- Groningen Machine for Chemical Simulation. It is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. <br> | ||
| * **GRO files**- GROMAC Format<br> | ||
| * **DCD** - Dynamics CoorDinate files<br> |
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| * **DCD** - Dynamics CoorDinate files<br> | |
| * **DCD** - trajectory format supported by CHARMM and NAMD (Dynamics CoorDinate) |
| * **RSMD**-Root Mean Square Deviation<br> | ||
| * **RSMF**- Root Mean Square Fluctuation<br> | ||
| * **PCS**- Principal Components analysis<br> |
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Please can you check spelling of these 3 abbreviations here?
| * **TRR**- trajectory file (coordinates and velocity) <br> | ||
| * **XTC**- trajectory file (coordinates only) <br> |
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mention here TRR and XTC are supported by GROMACS
| * **TRR**- trajectory file (coordinates and velocity) <br> | ||
| * **XTC**- trajectory file (coordinates only) <br> | ||
| * **ACPYPE tool**- AnteChamber Python Parser interface<br> | ||
| * **GROMOS**- GROningen Molecular Simulation<br> |
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| * **GROMOS**- GROningen Molecular Simulation<br> | |
| * **GROMOS**- force field (GROningen Molecular Simulation) |
can you make the same change for the next three force fields as well?
| * **AMBER**- Assisted Model building with Energy Refinement<br> | ||
| * **OpenFF**-Open Force Field<br> | ||
| * **TIP3P**- A water model that specifies rigid water molecules with charges and Lennard-Jones Paramenters assigned to each of the 3 atoms<br> | ||
| * **ITP files**- Atom Topologies (charges, mass, radii etc) <br> |
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mention it is a GROMACS file format
| * **NVT**- constant number (N), Volume (V) Temperature (T) <br> | ||
| * **NPT**- constant number (N) , Pressure (P), Temperature (T) <br> | ||
| * **NMR**- Nuclear Magnetic Resonance<br> | ||
| * **VMD**- Visual Molecular Dynamics <br> |
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| * **VMD**- Visual Molecular Dynamics <br> | |
| * **VMD**- Visual Molecular Dynamics, a visualization software |
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thanks @Ezichi-Fav! |
I updated the contributors.yaml file and Added a list of abbreviations with meanings to the High Throughput Molecular Dynamics and Analysis Tutorials (Computational Chemistry) in response to feedbacks.