TS-PPTIS (Transition State PPTIS)

Version 2.0

New python implementation of TS-PPTIS for Gromacs 5.X/2016/2018 and Plumed 2.X Based on scripts by G. Saladino and J. Juraszek @2014-2016

This version is UNDER DEVELOPMENT.

For reference see:

Juraszek J, Saladino G, van Erp TS, and Gervasio FL, "Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables." Phys Rev Lett. 2013 Mar 8;110(10):108106.

The code has been tested on Python 2.7.

Dependencies

• Numpy 1.11.0;
• MDTraj 1.8.0.

Utility Scripts Usage

A number of utility scripts are provided in the utils folder. Here is an example of a typical workflow.

First run the setup script to prepare all the necessary files, by giving as input information on the system (topology, coordinates, etc...) and the location of your local gromacs installation:

tsSetup.py -top topol.top -gro system.gro -mdp md.mdp -ndx index.ndx -gmx /usr/bin/gmx
           -win windowsList.dat -xtc traj.xtc -col COLVAR

The script will automatically store the information in a file (default: init.info) that is required to run the next set of scripts.

A text file windowsList.dat containing information on the windows to set up needs to be included. The format should be:

0.0,0.5,0.75
0.65,1.1,1.5
...

with each line containing a floating point representing the position of the left, centre and right window bounds, separated by a comma.

With tsSetup.py the TS-PPTIS windows are created. To set up a single run tsSetRun.py can be called. After running GROMACS,tsFinalize.py finalises the run in the single window. All they need is the init.info file and the tspptis window folder:

tsSetRun.py -info init.info -fold pptis00
[GROMACS]
tsFinalize.py -info init.info -fold pptis00

During the TS-PPTIS simulations, it is possible to monitor the windows with the tsReport.py utility. E.g.:

tsReport.py pptis*/

A standard analysis worfklow is available in tsAnalysis.py, which requires the path to the tspptis windows folders, a free energy profile (in Plumed 2 format), and an estimate of the TS. If none provided, the FES maximum will be taken as TS:

tsAnalysis.py -trans 1.55 -fes fes.dat pptis*/

Library Usage

Alternatively, you can use the library functions in a python script, which gives you more control on the tspptis parameters:

#Import the library
import tspptis as tps

#Initialise the system
ts = tsSetup('./topol.top',
             './system.gro',
             './md.mdp',
             './index.ndx',
             gmx='/usr/bin/gmx')

#Initialise a single window
ts.initWindow('./pptis10',
              [1.5,1.7,1.9],
             './traj_fixed.xtc',
              './COLVAR',
               overwrite=True)

#Setup the simulation for a specific window
ts.setUpTPS('../testfiles/pptis10')

#After the simulation terminates, finalize
ts.finalizeTPS('../testfiles/pptis10')

#Repeat the two steps above until convergence, then proceed to the analysis
tsa = tsAnalysis('./pptisoutput')

#Get probabilities and crossings analysis at a given TS of 1.25
tsa.getProbabilities()
tsa.getCrossings(1.25)

#Finally extract the Rates, after converting the fes if needed
fesList=plumed2List('./outputs/fes.dat')
tsa.getRates(fesList,valTS=1.25)

Contributors

• Federico Comitani (f.comitani@ucl.ac.uk)
• Giulio Mattedi (g.mattedi.16@ucl.ac.uk)