Getting Started¶
Requirements¶
Python > 3.9
gcc
g++
Installation¶
Run the following at the root directory of this repository
pip install CodeEntropy
Input¶
For supported format (AMBER NETCDF and GROMACS TRR) you will need to output the coordinates and forces to the same file.
For unsupported format see 1. Loading data for ideas on how to load custom data into MDanalysis universe and convert to supported format.
Units¶
The program assumes the following default unit
Qunatity |
Unit |
---|---|
Length |
Å |
Time |
ps |
Charge |
e |
Mass |
u |
Force |
kJ/(mol·Å) |
Quick start guide¶
Warning
This doesn’t work on Windows!!!
A quick and easy way to get started is to use the command-line tool which you can run in bash by simply typing CodeEntropyPoseidon
For help¶
CodeEntropyPoseidon -h
Arguments¶
Arguments |
Description |
Default |
Type |
---|---|---|---|
|
Path to Structure/topology file( |
Required |
list of |
|
Selection string for CodeEntropy such as protein or resid, refer to |
|
|
|
Start analysing the trajectory from this frame index. |
|
|
|
Stop analysing the trajectory at this frame index |
|
|
|
Steps between frame |
|
|
|
Temperature for entropy calculation (K) |
|
|
|
How many multiprocess to use. |
|
|
|
Name of the file where the text format output will be written. |
|
|
|
Name of the file where the total entropy output will be written. |
|
|
|
Name of the file where the residue entropy output will be written. |
|
|
|
Name of the file where certain matrices will be written. |
|
|
|
Name of the file where VMD compatible NMD format files with mode information will be printed. |
|
|
|
The 3 atom name in each residue for rotational and translational axis. |
|
list of |
|
Include cutoff shell analysis, add cutoff distance in angstrom. |
|
list of |
|
Reference molecule resid for system of pure liquid. |
|
|
|
Exclude a list of molecule names from nearest non-like analysis. |
|
list of |
|
Resname for water molecules. |
|
list of |
|
Include resname of solvent molecules (case-sensitive). |
|
list of |
|
Do entropy calculation at whole molecule level (The whole molecule is treated as one single bead.). |
Flag, activate when included |
Flag |
|
Do entropy calculation at residue level (A residue as a whole represents a bead.). |
Flag, activate when included |
Flag |
|
Do entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.). |
Flag, activate when included |
Flag |
|
|
|
|
|
Do solution entropy calculation at residue level (The whole molecule is treated as one single bead.). |
Flag, activate when included |
Flag |
|
Do solution entropy calculation at residue level (A residue as a whole represents a bead. |
Flag, activate when included |
Flag |
|
Do solution entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.). |
Flag, activate when included |
Flag |
|
Do solute contact calculation. |
Flag, activate when included |
Flag |
Example¶
# example 1 DNA
CodeEntropyPoseidon -f "Example/data/md_A4_dna.tpr" "Example/data/md_A4_dna_xf.trr" -a "C5'" "C4'" "C3'" -l "all" -t 8 --wm --res --uatom --topog 3
# example 2 lysozyme in water
CodeEntropyPoseidon -f "Example/data/1AKI_prod_60.tpr" "Example/data/1AKI_prod_60.trr" -l "protein" -b 1 -e 30 -d 2 --wm --res --uatom --topog 1 --solwm --solres --soluatom --solContact