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https://github.com/andreyrcdias/chitosan-in-water
https://github.com/andreyrcdias/chitosan-in-water
chitosan gromacs
Last synced: 16 days ago
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- Host: GitHub
- URL: https://github.com/andreyrcdias/chitosan-in-water
- Owner: andreyrcdias
- Created: 2024-12-05T17:51:39.000Z (28 days ago)
- Default Branch: main
- Last Pushed: 2024-12-13T11:51:02.000Z (20 days ago)
- Last Synced: 2024-12-13T12:36:39.641Z (20 days ago)
- Topics: chitosan, gromacs
- Language: Shell
- Homepage:
- Size: 84 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# chitosan-in-water
## Prerequisites
- [Gromacs](https://www.gromacs.org/)
- [curl](https://curl.se/)
- [make](https://www.gnu.org/software/make/)
## Quick Start
> [!TIP]
> You can run the commands sequentially by your own or run the shell script:
```bash
./run.sh
./run_v2.sh # to run using the 100k.gro file
```
> [!TIP]
> Also, if you want to clean the generated files, run:
```bash
./clean.sh
```
___
### Generate Topology
```bash
grep -v HOH filamento-chitosa.pdb > filamento-chitosa_clean.pdb
```
```bash
gmx pdb2gmx -f filamento-chitosa_clean.pdb -o filamento-chitosa_processed.gro -water spce
```
> We will use the all-atom **`OPLS`** force field, so type **`15`** at the command prompt, followed by `Enter`
> [!NOTE]
> We already have the generated topology, [`100k.gro`](100k.gro) is equivalent to `filamento-chitosa_processed.gro` (I guess)
### Simulating a simple aqueous system
```bash
gmx editconf -f filanemnto-chitosa_processed.gro -o filanemnto-chitosa_newbox.gro -c -d 1.0 -bt cubic
```
```bash
gmx solvate -cp filanemnto-chitosa_newbox.gro -cs spc216.gro -o filanemnto-chitosa_solv.gro -p topol.top
```
### Add Ions
```bash
curl -O http://www.mdtutorials.com/gmx/lysozyme/Files/ions.mdp
```
```bash
gmx grompp -f ions.mdp -c filanemnto-chitosa_solv.gro -p topol.top -o ions.tpr
```
```bash
gmx genion -s ions.tpr -o filanemnto-chitosa_solv_ions.gro -p topol.top -pname NA -nname CL -neutral
```
> When prompted, choose group **`13 "SOL"`** for embedding ions. You do not want to replace parts of your protein with ions.
### Energy Minimization
```bash
curl -O http://www.mdtutorials.com/gmx/lysozyme/Files/minim.mdp
```
```bash
gmx grompp -f minim.mdp -c filanemnto-chitosa_solv_ions.gro -p topol.top -o em.tpr
```
```bash
gmx mdrun -v -deffnm em
```
### Equilibration
#### Phase 1
```bash
curl -O http://www.mdtutorials.com/gmx/lysozyme/Files/nvt.mdp
```
```bash
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
```
```bash
gmx mdrun -v -deffnm nvt
```
#### Phase 2
```bash
curl -O http://www.mdtutorials.com/gmx/lysozyme/Files/npt.mdp
```
```bash
gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
```
```bash
gmx mdrun -v -deffnm npt
```
### Production MD
```bash
curl -O http://www.mdtutorials.com/gmx/lysozyme/Files/md.mdp
```
```bash
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
```
```bash
gmx mdrun -v -deffnm md_0_1
```
### Analysis
```bash
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center
```
```bash
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
```
```bash
gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns
```