First Molecular Dynamic Simulation
Step-7. Production MD

Pietro Buffa

The system is finally ready. We can now release the position restraints and start MD for data collection. The procedure is quite similar to the previous step but, with an exception, the time necessary to obtain the final result will be much longer now (almost 35 hours on a dual-processor AMD Opteron 2Ghz with Linux CentOS). We want to run 1ns MD simulation in total but we spent 200ps for the two previous equilibration steps. The "real" MD that we can use for data collection will be 800ps. Download [here] the .mdp file that we are going to use in this step, save it into your work directory and run the two previous tools again:

> grompp -f md.mdp -c eq2.gro -p topol.top -o md_01.tpr

> mdrun -v -s md_01.tpr -o md_01.trr -e md_01.edr -c md_01.gro -g md_01.log -cpi eq2.cpt -cpo md_01.cpt -x md_01.xtc

We have a new file .xtc this time, what is this? Trajectory files (the coordinates over time), are written initially by mdrun to contain atomic positions, velocities, and forces. The type of data and the period with which they are written are controlled with .mdp file options. Gromacs will write full-precision portable-binary data in a format known as a .trr file and, optionally, a reduced-precision format for positions only, known as an .xtc file, useful for the analysis.

Go to the Step-8.

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