How to run a complete simulation

Theory

The .pdb is generated from X-ray diffraction crystallography. This process requires a crystal of the protein, which occurs only at low temperature (~5°K). Taking this in consideration, we have to go through different steps to bring our protein to lab conditions.

First minimisation

We start with a few minimization rounds, to reach a minmimum in the sens of potential energy.

Heating

When the protein is stable, we have to add heat (kinetic energy) to reach an higher temperature (~300°K). We have to take a special care not to add heat too fast resulting in protein burst.

First NPT

This is a relaxation step, with constant atom number, pressure and temperature. This is a kind of homogeneization of distribution of the atoms inside our box.

NVT

This is also a relaxation step, with constant atom number, volume and temperature.

Second NPT