A Technical Introduction to the MD-OPEP Simulation Tools

Jessica Nasica

Université de Montréal

Montréal, Québec, Canada

Outline

Overview of the simulation method Why use “simulator”? The OPEP force-field Running the simulation: what you need to get started The simulation step by step The output of the “simulator” The analysis tools

The PTWHAM analysis The RMSD analysis Secondary structure tools Contacts tools Clustering tools Graphical tools and various useful scripts

The simulation method

REMD simulation ( Replica Exchange Molecular Dynamics )

A simplified coarse-grained potential: OPEP

Why use “simulator”?

It can be used: To study aggregation processes To check for the stability of a particular molecular

assembly

The simplified force-field allows to reach bigger time scales more efficiently:

To study long-range proteins motions To extract accurate thermodynamics properties

P. Derreumaux, N. Mousseau – J. Chem. Phys. 126, 025101 (2007)

The OPEP force-field

OPEP = Optimized Potential for Efficient structure Prediction

Reduced-protein model: A 6-particle model with a

detailed representation of the backbone (except for Proline)

Each side chain is represented as one particle and defined by one centroid

Implicit solvent solvent effects included in the interaction parameters

Maupetit et al. - Proteins 2007; 69:394-408 / Chebaro et al. – J. Phys. Chem. B 2008

The OPEP force-field

OPEP energy function:

Local Forces:Includes changes in bond lengths and valence angles for all

particles and changes in improper torsions of the side chains. Nonbonded Forces:

Van der Waals, electric and hydrophobic forces short- and long- range interactions are computed separately.

Use of a pairwise contact potential between side chains represented either by a 12-6 potential or by a 6-potential.

Hydrogen-bonding Forces:2 terms 2-body H-bonds

4-body effects = cooperative energies between H-bonds

bondHnonbondedlocal EEEE

Maupetit et al. - Proteins 2007; 69:394-408 / Chebaro et al. – J. Phys. Chem. B 2008

Running the “simulator”

What you need to get started: The executable file after compilation of the code The parameter file ‘simulator.sh’ Your ‘.pdb’ file in an OPEP format The corresponding topology file (.top), residue

description file (.list) and ‘ichain.dat’ file The ‘cutoff.dat’ and ‘scale.dat’ files A link file and a qsub script

The simulation step by step

Step 1:Minimization: finding a stable starting pointIt makes sure that the structure’s energy is minimized using ART.

The 2 phases of ART:

-Activation phase the structure is pushed towards a saddle point

-Relaxation phase the structure is pushed slightly over the saddle point and relaxed to a new local energy minimum

Mousseau et al. – Frontiers in Bioscience 13 - 2008; 4495-4516

At the saddle point:

0__ atomeachonF

The simulation step by step

Step 1:Minimization: the outputThe minimized configuration is written in the file “relaxed_conformation.pdb”.The data resulting from each minimization step is written in “log.file”:

Total Energy . towards a minimum

Net Force to 0

Decrease in potential energy

term

Velocity

Decrease in kinetic energy term

Rmsd value

Structure is undergoinga configurational change

The simulation step by step

Step 2: Thermalization:It thermalizes the configurations by heating up by stages until it reaches the target temperature.

Here, in “simulator.sh”:

Initial conformation Relaxed conformation(from minimization step)

Thermalization conformations

1 5

E1 = -93.859T1 = 59.25 K

E =T =

-98.52900.00 K

E2 = -94.2221T2 = 88.88 KE3 = -72.7113T3 = 133.32 KE4 = 25.8615T4 = 199.98 KE5 = 103.8417T5 = 299.97 K

Energies are in Kcal/mol

The simulation step by step

Step 3: MD calculation of forces:using the velocity-Verlet algorithm for integrating Newton’s equation of motion for each particle:

where , the force on particle i.iii amF i

i r

VF

(Highly simplified description of MD)

The simulation step by step

Step 4: Writing of the .pdb files:At each desired time step, the new configuration is written in the “min” files for each temperature.

Output files

The configurations are sorted by temperature.

Analysis tools

The PTWHAM tool

Allows a temporal correlation in the data, using autocorrelation analysis, to compute equilibrium averages.

we can derive thermodynamical properties, including data from each temperature.

The PTWHAM tool

How to use it:

1) ./ptwham_first will read data in each pXX/min file, calculate the Rg, rmsd and end-to-end distance, and output files simXX.txt, wham_parameters.dat, beta.dat

2) edit wham_parameters.dat

3) ./ptwham_second mintime maxtime writes “averages.txt” containing U (total energy), rmsd, Cv, end-to-end distance, writes “free_energies.txt” containing Uk (average energy per replica), free energy and entropy and writes “deviations.txt” containing all the uncertainties on the above observables.

The PTWHAM tool

The output:Using 2 python scripts, we obtain the following plots:

The RMSD tool

Calculates the rms distance between 2 configurations or between 1 configuration and a list of configurations taking into account their individual clusters for more accuracy.

Recognizes clusters from hydrogen bonds formed using the DSSP definition of a hydrogen bond:

the DSSP algorithm identifies a H-bond if E<-0.5 Kcal/mol.

The program searches all the peptides forming H-bonds and rearranges the pdb file accounting for the chain order in the clusters formed.

How to use it: rmsd conf1.pdb list

It needs “ichain.dat”.

The RMSD tool

The output files are :- rmsd.txt containing all the rmsd values for each configuration in the list- id_order.txt containing all the clusters formed for each configuration in the

list- parallel_planes.txt containing a list of all the clusters being parallel to each

other

The Replicas tool

A python script that generates a graph showing acceptance probability for replica exchange.

Need “log.file” and “replicas.dat”

Additional useful scripts

Pymol scripts allowing to prepare the pdb files and make movies out of the configurations unique_pymol

command: unique_pymol file skip Python scripts:

extract_confs extracts a subset of configurations from a single file containing a list of configurations.

repair_min repairs min files that are broken by a crash, removing all the incorrect lines.

Graphics scripts: trace_averages.py ( WHAM analysis )

command: ./trace_averages.py “averages.txt” “title” “1” trace_freeenergies.py ( WHAM analysis )

command: ./trace_freeenergies.py “free_energies.txt” “title” “1”

Where to find our packages?

You will find an updated version of the analysis tools on the wiki:

http://riel.pmc.umontreal.ca/groups/biophysique/

Thank you !