MD: Plain run

Introduction

How setup a MD simulation in water. Plain MD protocol

Setup of the environment

Open a terminal in the server (this instruction depend on the configuration of the server)

Setup the environment of the terminal

If a setup file is present it is possible to use the instruction source

In this case the setup file is located in the HOME directory and is named gromacs_setup.source

Setup of the MD protocol

Download the scripts

Untar the files

All the necessary files are in the directory

• mdp files contain gromacs instructions
• sh files are scripts that launch gromacs

To run the MD protocol, two additional files are required:

• the starting file (file.gro)
• the topology file (file.top)

These two files are prepared following other instructions (e.g. MD cylici peptides setup, see the index for other setup protocols)

Run the MD

The scripts must be modified with a text editor changing the name of the input files in the sh files

• the correct topological file should be written in all sh files
• the gro initial file should be written in em.sh
• the correct name should be written in run_fix2.sh
• the scripts use conventional names for the other files that have to be passed in the various steps of the protocol

Firstly, run the minimization script

The minimization is fast and allows to verify that all is ok.

If the minimization finishes without errors, it is possible to run the complete MD sequence

Then gromcas runs and write messages in rur_run.log.

It is possible to close the terminal and logout form the server.

The results of the MD can be visualized using VMD

Where initialfile.gro is the starting structure and finaltraj.xtc is the centered trajectory resulting from run_fix2.sh script.