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First Molecular Dynamic Simulation
Step-6. Equilibration

Pietro Buffa

Now, after EM, we should have a reasonable starting system. If we were to attempt unrestrained dynamics at this point, the system could collapse. In order to put our system in the best conditions, we have to equilibrate the solvent and the ions arround the protein and to increase the temperature of the system until the value that we established. After the system arrives to the right temperature, we will apply pressure until it reachs the proper density.

Do you remember the "posre.itp" file that the Gromacs tool pdb2gmx generated at the beginning? Well, this file assumes a big value at this point because it allows to apply a position restraining force on the heavy atoms of the protein in order to allow us to equilibrate our solvent arround the protein without added structural changes in the protein. Movements are permitted but only after overcoming a substantial energy penality.

We are going to lead this step under the canonical NVT ensemble (Constant Number of particles, Volume and Temperature). In such a system, the temperature should reach a plateau at the desired value and it requires in general 50-100 ps. In this tutorial, we will perform a 100 ps NVT equilibration. Depending of your workstation, this step could take time (almost three hours on a dual-processor AMD Opteron 2Ghz with Linux CentOS). 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 equilib-NVT.mdp -c em.gro -p topol.top -o eq.tpr

> mdrun -v -s eq.tpr -o eq.trr -e eq.edr -c eq.gro -g eq.log -cpo eq.cpt

At the end of the process, if everything is alright, we will have six new files:

eq.trr
eq.edr
eq.gro
eq.log
eq_prev.cpt
eq.cpt

Four of them we have already known, the files "eq_prev.cpt" and "eq.cpt" are still unknown. They are called check-point files and Gromacs writes them every 15 minutes in order to allow you to recover your MD after a potential problem (blackout for example) or simply, continue from a previous step.

As usual, we can analyze the .edr file using the following Gromacs tool:

> g_energy -f eq.edr -o temperature.xvg

At the prompt type "15 0" to select Temperature (15) and to finish (0). For a graphical presentation of these data:

> xmgrace temperature.xvg

Now, we need to perform other 100 ps of equilibration to set the pressure of the system under the canonical NPT ensamble (Constant Number of particles, Pressure and Temperature). To this end, we need to use another mdp file which contains some new settings. 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 equilib-NPT.mdp -c eq.gro -p topol.top -o eq2.tpr

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

In this last step, we are saying to mdrun to start working from the last equilibration (-cpi eq.cpt) and go on with the second step equilibration, generating a second check point file (-cpo eq2.cpt).

As usual, we can analyze the .edr file using the following Gromacs tool:

> g_energy -f eq2.edr -o pressure.xvg

At the prompt type "15 0" to select Pressure (15) and to finish (0). For a graphical presentation of these data:

> xmgrace pressure.xvg


Go to the Step-7.

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