ZEPHYR + GROMACS José R. Valverde CNB/CSIC jrvalverde@cnb.csic.es MD tutorial ZEPHYR + GROMACS José R. Valverde CNB/CSIC jrvalverde@cnb.csic.es © José R. Valverde, 2014 CC-BY-NC-SA

Simulation in vacuo

Getting started Open a terminal and type “zephyr &”

Zephyr main window Zephyr offers a GUI to simplify running standard MD simulations using GROMACS. You can select the starting configuration as a PDB file By default it offers a tutorial example: alanylalanine You can select the output directory Results will be saved in a sub-directory of it By default it offers “zephyr_sims” on your home. Procceed to “Parameters”

MD parameters Here you can select the parameters that will drive the MD simulation. Whether a minimization should be done first Length and time step. Temperature (in various scales) and force field Solvent viscosity and implicit water model (more or less accurate) Sampling periodicity (how often to save configurations) Uncheck VMD and proceed to “Simulation”

Create working directory Your simulation will be saved on a specific subdirectory named after the starting PDB file. It will be placed below the directory you originally selected, thus for our example ~/zephyr_sims/alanylalanine_capped All resulting files will be found there

Simulation run Zephyr now proceeds to invoke GROMACS to run the simulation Depending on your choice of parameters it may run faster or slower. This one should go very fast! IFF YOU HAVE VMD installed and configured, you can use it to monitor directly the progress of the simulation visually as it runs.

Wait... This can be the most tiresome part of the work. You must wait for the computer to finish the calculations Depending on your option choices and hardware, this may require up to several months of calculations! So... you better get the simulation parameters right from start!

View the trajectory Inspect the trajectory using UCSF Chimera Close Zephyr (close the window --“x”) Open UCSF Chimera Go to the Tools menu and select MD/Ensemble Analysis A sub-menu pops up, choose “MD movie”

Opening a trajectory Now we need to open the trajectory data: MD simulation parameters TPR file Time-step, simulation length, box size, conditions... Sampled values TRR file / XTC file Coordinates, Energies, etc... Select the newly generated TPR file zephyr_sims/alanylalanine_capped/......tpr

Load the trajectory Open the corresponding TRR file Make sure it matches the TPR file you selected earlier In other words: the parameters and the trajectory must correspond to each other.

Play You can now view the progression of the simulation Once or many times (loop) At various speeds Displaying only one every so frames You can carry out and plot several analyses You can even create a movie

Continuation run

Continuation runs Sometimes simulations are too short You could not detect an interesting phenomenon You could not run a longer simulation The simulation was stopped by external forces... You can use a previous run as the starting point and extend it for longer periods Open Zephyr Choose Trajectory File (.trr) from previous run alanylalanine_capped_processed_box.em.md.trr

Choose parameters and length If you did run your simulation with Zephyr, it is usually better to let Zephyr “Auto load mdp params” If that fails or you used tailored parameters, you may need to click “Load mdp now” to choose them Select the total time to simulate in the continuation run Click on “Continue simulation”

Explicit solvent model

Explicit solvent The previous run used an implicit solvent model I. e. water molecules were not actually there, but their effect was simulated by increased viscosity We did not consider solvent electrostatic effects (e.g. water has a dielectric constant of 80) We can ask Zephyr to make and solvate a box for us, filling it with explicit water molecules at random coordinates, and equilibrate charges with ions. Click on “Use explicit solvent”

Reduce simulation time Adding water will increase the number of atoms to model Running time grows roughly with the square of the number of atoms When using solvent, membrane, etc... we will need to adjust the simulation time TIP: start with a short run to verify everything is OK and the continue it as needed Select “100” steps.

Wait After clicking “Simulate” the process will be started This time the system is considerably bigger Steps will take longer You may be able to see that there is a preparation, a minimization and the actual MD run.

Long running times As you can see, when the model size grows, time also grows, and to a larger extent. For complex models, it may require specialized hardware GPUs (note that you can select it in the parameters window) Clusters (in this case you will need to run the simulation manually) In large cases you will likely fine-tune parameters and split the run in “pieces” or “sessions”

Visualize the system This is a very short run, so we will not have a meaningful trajectory But we can see what Zephyr did to our system: Open UCSF Chimera Open the Gromacs file used for the run alanylalanine_capper_processed.box.wat.ion.em,gro See how Zephyr/GROMACS created a box filled with water molecules and ions around the molecule.

Fine-tuning simulations

Fine tuning simulations Open Zephyr once more Proceed to parameters Click on “Advanced Parameters” Inspect the options. Look at alternative nominal values You can save the fine-tuned parameters to a file and use it later in subsequent simulations. You can load a previous parameter file and use or modify it.

Going pro... You can look at the saved parameter files with any text editor and hand-modify them You can look at the coordinate files with any text editor and hand-modify them Useful to adapt atom names to FF expectations You can generate advanced models with other tools Check out PACKMOL http://www.ime.unicamp.br/~martinez/packmol/ Read GROMACS manuals and tutorial www.gromacs.org

That was all just the beginning folks! Image by Web-Master. CC0. http://pixabay.com/en/danger-bridge-broken-bridge-178132/