Simulating a Peptide with GROMACS

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Introduction

Setting up the Parallel Environment

Obtaining Curriculum Module

Passwordless SSH

MPI Environment

GROMACS Environment

Simulation

Generating a Topology File

Using pdb2gmx to make a .top and a .gro from a .pdb.

Create an Empty Bounding Box

Creating an empty box around the peptide with editconf.

Solvate

Fill the empty box with water using genbox.

Energy Minimization

Reduce strain caused by the addition of hydrogen and bad Van der Waals contacts caused by particles that are too close. First step in making the system sane. Grompp then mdrun. Magic is in the .mdp file. Use g energy to see results.

Equilibration

Correct velocity distribution to simulate a valid statistical ensemble (look at more). Grompp and mdrun.

MD Without Restraints

Full MD with grompp and mdrun.

Analysis Of Output

View Trajectory

View with ngmx.

Changes in Molecule Structure

Root mean square deviation to view changes in molecular structure (g_rms). View the graph (xmgrace?).

Changes in Molecule Size

Graph of changes in the size of the molecule with g_gyrate. View the graph (xmgrace?).