Temperature generator for REMD-simulations

WARNING

As of 2021, the temperature generator for REMD-simulations web server is no longer online, but its source code is available at https://github.com/dspoel/remd-temperature-generator. In order to run it, you must install php-cli (apt install php7.4-cli), open a console on the source directory, and run php -S localhost:8000. You can then access the server on your browser going to http://localhost:8000, fill in the parameters and click submit to get the temperatures.

If you still want to use this python library, after running the server as described above, update the TGENERATOR constant at https://github.com/mchelem/remd_temperature/blob/master/remd_temperature.py#L25 to TGENERATOR_URL = 'http://localhost:8000/tgenerator.php' and then run the examples below.

Intro

Python library to obtain temperatures for replica exchange molecular dynamics simulations. This library queries the Temperature generator for REMD-simulations web server.

Temperature generator for REMD-simulations is a web server for generating temperatures for REMD-calculations. You submit the number of protein atoms and water molecules in your system, and an upper and lower limit for the temperature range, information about constraints and/or virtual sites and a desired exchange probability Pdes, and the webserver will predict a temperature series with correspondig energy differences and standard deviations which matches the desired probability Pdes.

Reference: Alexandra Patriksson and David van der Spoel, A temperature predictor for parallel tempering simulations Phys. Chem. Chem. Phys., 10 pp. 2073-2077 (2008) http://dx.doi.org/10.1039/b716554d.

Installation

Run the following command:

pip install git+https://github.com/mchelem/remd_temperature

Usage

Get temperatures and energies (table on the image below):

from remd_temperature import get_temperatures_energies
params = {'number of protein atoms': 200}
print(get_temperatures_energies(params))

Get temperatures only (last line on the image below):

from remd_temperature import get_temperatures
params = {'number of protein atoms': 200}
print(get_temperatures(params))

See also the examples, for details on how to handle the output. The parameters are the ones available at http://folding.bmc.uu.se/remd/

You can use either human readable names (label) or shorter and less explanatory form input names. You cannot mix both formats in the same input.

For example, here are two valid and equivalent ways to set contraints in water :

# Uses human readable format
params = {'constraints in water': 'bonds to hydrogens only'}  

OR

# Uses original web form parameters
params = {'WC': 1} #

Here are the mappings between human readable and form variables (the latter in bold):

• Exchange probability: Pdes,
• Lower temperature limit: Tlow,
• Number of water molecules: Nw,
• Number of protein atoms: Np,
• Hydrogens in protein: Hff, Values: 0 (All H), 1 (Polar H),
• Simulation type: Alg, Values: 0 (NPT), 1 (NVT),
• Tolerance: Tol,
• Upper temperature limit: Thigh,
• Constraints in water: WC, Values: 0 (Fully flexible), 2 (Flexible Angle), 3 (Rigid)
• Constraints in the protein: PC, Values: 0 (Fully flexible), 1 (Bonds to hydrogens only), 2 (All bonds)
• Virtual sites in protein: Vs, Values: 0 (None), 1(Virtual hydrogen)