1. PeptideSim

• 1. Release Notes
• 2. Installation
  • 2.1. Bluehive Install
• 3. Running Tests
• 4. Developer Test Environment
  • 4.1. Creating Docker Image
  • 4.2. Running Unit Tests
  • 4.4. Running Unit Tests Interactively
• 5. Example Workflows
  • 5.1. NVT simulations with multiple peptides
    • 5.1.1. Imports
    • 5.1.2. Input Conditions
    • 5.1.3. Simulation Steps
    • 5.1.4. Run the script
    • 5.1.5. Saving at intermediate steps
  • 5.2. Enhanced Sampling (PT-WTE)/ Experiment Directed simulation (EDS)
• 6. Restarting Simulations

1. Release Notes

See Changelog

2. Installation

2.1. Bluehive Install

1. Load required modules

module load anaconda3 packmol libmatheval gromacs-plumed/2019.4/b2 openblas git

2. Create a virtual environment

conda create -n yourenvname python=3.7

Peptidesim is no longer available for python2 versions. Once you create your environment, you should activate it for the next steps:

source activate yourenvname

Check on pip and python and make sure they are sourced to your environment directory:

which pip #or which python
# The output should look like this:
# /.conda/envs/yourenvname/bin/pip

Note: In case the environment is not properly activated, i.e., which pip outputs a path not as mentioned above, try conda init. Close and reopen a new terminal and do conda activate <yourenvname>.

3. For installing PeptideSim, you need to clone the package from github.

git clone https://github.com/ur-whitelab/peptidesim.git

Change directory to package and install the requirements and the module:

cd package
pip install -e .

4. Setup a config file for Gromacswrapper to be able to find the gromacs installation. You can use the one given below and save it to ~/.gromacswrapper.cfg

.gromacswrapper.cfg

 [ DEFAULT ]
 qscriptdir = %( configdir )s/qscripts
 templatesdir = %( configdir )s/templates
 configdir = ~/.gromacswrapper
​
 [ Gromacs ]
 release = 2019.4
 gmxrc = /software/gromacs-plumed/2019.4/b2/bin/GMXRC
 extra =
 tools = gmx gmx_mpi
 groups = tools
​
 [ Logging ]
 logfilename = gromacs .log
 loglevel_console = INFO
 loglevel_file = DEBUG

Alternatively, on a non-head node use interactive python to do this:

import gromacs
gromacs.config.setup()

3. Running Tests

You must install pytest first, then you can run the tests using the following command:

python -m pytest -x -v  peptidesim/package/tests/

You should be on an interactive node if on bluehive. The tests generate a lot of files, so run it in a clean directory.

4. Developer Test Environment

4.1. Creating Docker Image

Load the plumed gromacs docker image from dockerhub:

docker pull whitelab/plumed-gromacs

Now we build the peptidesim testing image

cd test-docker
docker build -t peptidesim/test .

These two steps gather the plumed and gromacs version. Generally, you do not need to re-run them.

4.2. Running Unit Tests

From the repo root directory:

[sudo] ./test.sh

You may need to have sudo depending on your docker configuration. This will run all tests and clean-up. If are using Windows or need to modify the command, use:

docker run -it --rm -v [path_to_peptidesim_root]:/home/whitelab/peptidesim peptidesim/test

4.4. Running Unit Tests Interactively

If you want to leave all test files around and have python access to troubleshoot, including an editable install so code you change is reflected, use:

[sudo] ./interact.sh

Type exit to leave the docker environment. See instructions that are printed after running the command for how to interact/use the environment.

5. Example Workflows

5.1. NVT simulations with multiple peptides

A complete example can be found in peptidesim/inputs/simple.

5.1.1. Imports

Create a Python script simple.py and import the PeptideSim class

from pepsidesim import PeptideSim

5.1.2. Input Conditions

Specify peptides, conditions, and initialize. Note that all properties of the PeptideSim have defaults, so you do not necessarily need to specify a concentration or water model.

seq = 'EKEKEKEKEKEK' # input the sequence in one-letter-code
name = 'EK6' # naming the sequence
pep_copies = 1 # specify the number of copies, increase the number if running multiple chains to study self assembly and etc.
ps = PeptideSim(name, [seq], [pep_copies], job_name='2mer_{}'.format(name)) # input to PeptideSim
ps.peptide_density = 0.008 # g/mol
ps.water = 'spce' # specify water model
ps.mpi_np = 4 # Number of MPI processes to use
ps.initialize()

5.1.2.1 Using Arbitrary Forcefields

In case you want to use a forcefield X that is not available in GROMACS, add the forcefield files to the peptidesim object and put it in the peptide_structures directory. Then use the pdb2gmx_args input options to select the forcefield.

ps.add_file('path/to/forcefieldX.ff')
ps._put_in_dir('peptide_structures')
ps.forcefield = 'select'
ps.water = 'select'
# Specify input options, here ('1', '1') are the strings you would enter for the
# forcefield and water, respectively, when using gmx pdb2gmx command interactively.
ps.pdb2gmx_args['input'] = ('1', '1')

Note that if you want to use a water model that's not available in GROMACS, you need to provide the water_model.gro file to solvate the system. You will have to change the source code function _solvate() in /package/peptidesim/peptidesim.py to specify this new water file.

5.1.3. Simulation Steps

Here we do energy minimization, annealing and NVT equilibration. Note that we can pass specific gromacs mdp arguments as python objects. The tag is the short name of the simulation we are doing. The mdpfile names used here are templates found in the peptidesim package. You can provide your own files if desired.

ps.run(mdpfile='peptidesim_emin.mdp', tag='init_emin', mdp_kwargs={'nsteps': 10**5})
ps.run(mdpfile='peptidesim_anneal.mdp', tag='anneal_nvt')
ps.run(mdpfile='peptidesim_nvt.mdp', tag='nvt_prod', mdp_kwargs={'nsteps': int(3 * 5*10**5), 'constraints': 'h-bonds'})

5.1.4. Run the script

If you are using a slurm job script, you could use this example:

#!/bin/sh
#SBATCH --partition=standard --time=120:00:00 --output=EK6.txt
#SBATCH --mail-type ALL
#SBATCH -N 2

python simple.py

5.2. Enhanced Sampling (PT-WTE)/ Experiment Directed simulation (EDS)

A complete example can be found in peptidesim/inputs/pte.

6. Restarting Simulations

Restarting is handled via the built-in gromacs restarts combined with python pickle objects. After each modification of the simulation (e.g., initialization or running a simulation), a current pickle file is saved in the peptidesim root directory. Its name matches your job name. Additionally, previous pickle files are saved in a directory called restarts that can be used to resume from previous stages. Your current pickle is always saved there too, so that you can simply move a pickle file from this directory to your root directory to restart from a different step. Pickle files are automatically used to restart your simulation in a script and simulations that have already completed will be skipped so that you need not edit your script if restarting.

You can disable restarting by passing the restartable=False argument to the PeptideSim initialization. If the restartable flag is not set but there are existing pickle objects, an error will occur to prevent you from accidentally overwriting a previous simulation.

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© Andrew White at University of Rochester