Enhanced-Sampling-in-AMBER-tutorial

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Enhanced-Sampling-in-AMBER-tutorial

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Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)

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# Enhanced-Sampling-in-AMBER-tutorial
Tutorials on AMBER based Metadynamics and Gaussian Accelerated MD (GaMD) simulations on Chignolin.
For running AMBER metadynamics, please refer to the first half of this [video](https://youtu.be/UFqUJcnxXUQ?feature=shared)

## General information
1. ````chignolin.pdb````, ````chignolin.prmtop```` and ````chignolin.rst```` are the input files required for the AMBER simulation.
2. ````md.in```` is the AMBER run file, which contains the details of the simulation. The parameters that you can vary are \
   a. ````ntpr = 500   ! write energy information every 500 steps to log file```` \
      ````ntwx = 500   ! write coordinates every 500 steps to a trajectory file```` \
      ````ntwr = 500   ! write restart file every 500 steps to corresponding file ````
      
   b. ````nstlim = 2000000 ! perform 2000000 MD steps```` \
      ````dt = 0.002     ! use time steps of 2fs````

## Metadynamics 
1. Apart from the above input files, a ````plumed.dat```` file is also important, as it has the information about the paramters to be used in a metadynamics simulation. An example file has been given in this repo.
2. To run PLUMED on AMBER, the following commands are required in md.in: \
     ````plumed = 1 ! Plumed will run```` \
     ````plumedfile="plumed.dat" ! Name of the plumed.dat which AMBER has to access````
3. To run the simulation after preparing all the files, run ````sbatch run.sh````. The ````run.sh```` should contain the AMBER run command, the ````export PLUMED_KERNEL```` command and all the relevant modules and SBATCH headers. An example file has been provided.
4. 2 PLUMED output files will be produced. ````COLVAR```` file will have the information about the collective variables and the bias added, while ````HILLS```` file will have the details of the gaussian bias potentials that were added over the simulation.
5. Run ```` plumed sum_hills --hills HILLS --mintozero --min 0 --max 10 --bin 200```` to get the ````fes.dat```` file that has the reweighted free energy profile.

## Gaussian Accelerated Molecular Dynamics (GaMD) 
1. To run GaMD on AMBER, additional commands have to be added to md.in (Please see the ````!! GAMD settings```` section of ````md.in```` in the GaMD folder of this repository)
2. To run the simulation after preparing all the files, run ````sbatch run.sh````. The ````run.sh```` should contain the AMBER run command and the relevant modules and SBATCH headers. An example file has been provided.
3. 2 GaMD output files will be produced. ````gamd.log```` is the file that stores all the potential energy information through the simulation, and ````gamd-restart.dat```` are the [GaMD parameters](https://pubs.acs.org/doi/10.1021/acs.jctc.5b00436) that the simulation uses.
4. Run the command ````cpptraj -i analysis.cpptraj```` to get the ````rmsd.dat```` and/or ````rg.dat```` (Radius of gyration) information from the simulation. You have to do ````conda activate AmberTools23```` in order to access the ````cpptraj```` command.
5. For reweighting to get the free energy surface (FES): \
   a. Get weights.dat from gamd.log using the command ````awk 'NR%1==0' gamd.log | awk '{print ($8+$7)/(0.001987*300)" " $2 " " ($8+$7)}' > weights.dat```` \
   b. Get output.dat from rmsd.dat and rg.dat (If using 2 progress coordinates for a 2D surface) using the command ````awk 'NR==FNR{a[NR]=$2; next} {print a[FNR], $2}' rmsd.dat rg.dat > output.dat```` \
   c. Run the command ````./reweight-2d.sh 50 50 0.1 0.1  output.dat 300````, where 50 50 are the cutoffs for both progress coordinates, 0.1 0.1 are the bin spacings, and 300 is 300 K.

## Exercise
After running the Metadynamics and/or GaMD simulation, write **Python codes** to read the free energy data files, and plot the free energy profiles (Hint: NumPy and Matplotlib should be enough ; use ````np.genfromtxt```` to read the files). \
Which Enhanced Sampling method performs better?

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