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Goal: Produce A Stable Molecule To Simulate: GMX Editconf - F Molecule - PDB - o Molecule - Gro - Box LX Ly LZ

The document provides instructions for generating a stable molecule and box of molecules for simulation in GROMACS. It describes using gmx editconf to generate a molecule.gro file with the molecule in a box, gmx grompp to generate topology files, and gmx mdrun to minimize the energy and stabilize the molecule. It then explains using gmx insert-molecules to add multiple copies of the molecule to a box.gro file and incrementally increasing the density and minimizing again until reaching the desired density for simulation.

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35 views2 pages

Goal: Produce A Stable Molecule To Simulate: GMX Editconf - F Molecule - PDB - o Molecule - Gro - Box LX Ly LZ

The document provides instructions for generating a stable molecule and box of molecules for simulation in GROMACS. It describes using gmx editconf to generate a molecule.gro file with the molecule in a box, gmx grompp to generate topology files, and gmx mdrun to minimize the energy and stabilize the molecule. It then explains using gmx insert-molecules to add multiple copies of the molecule to a box.gro file and incrementally increasing the density and minimizing again until reaching the desired density for simulation.

Uploaded by

chandralove
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as ODT, PDF, TXT or read online on Scribd
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Goal: Produce a stable molecule to simulate

Well, you should now have a PDB and an ITP. We will now put one molecule in a big box to be sure
that the molecule is stable. If it expoltoes it is not worth to go any further. We will thus generate a
*.gro file which is the kind of molecular files to feed GROMACS. The syntaxis is:

• gmx editconf -f molecule.pdb -o molecule.gro -box Lx Ly Lz

where molecule.pdb is the input molecule and molecule_eq.gro is the equilibrated molecule. Lx, Ly
and Lz are the lengths of the box. Now we should have the molecule in a box (molecule.gro) a force
field file (molecule.top) and we have to add a file that tells gromacs what to do (an mdp file). You
can find one here but be sure to change the integrator md (used to do an MD simulation) to steep to
minimize the energy.We will call this file min.mdp Then with:

• gmx grompp -f min.mdp -c molecule.gro -p molecule.top -o mol_eq.gro

The files should be ready to use. To actually do the simulation use

• gmx mdrun

And everything should work...

Goal: to generate a box with the right number of molecules

Now we will produce the actual box to simulate. Fist of all you should have to decide a size of your
box that is compatible with the density of your system. The problem will be to fit the molecules in
the box. For this reason is better to start with a big box (a lower density) and then increase the
density at small steps. Let's assume that you want to simulate 125 molecules in a box of 50 AA with
a density of 1000g/l. Be aware that unit in GROMACS are Nm! First we will change the size of the
box with one molecule so that it is big enough to fit all molecules you want to add. "Big enough"
means that the program does not complains because he couldn't put all molecules into the box.:
• gmx editconf -f mol_eq.gro -o mol_eqb.gro -box 5 5 5

We will then add 124 molecules to the box with:


• gmx insert-molecules -f mol_eqb.gro -ci mol_eqb.gro -o box.gro -nmol 124 -rot xyz -try
100
Since we want to insert the same molecule (mol_eqb.gro) to the existing file mol_eqb.gro the
configurations to be inserted and inserted are the same. We will also insert molecules randomly
rotated with -rot, and will try 100 times to insert the molecules. After that you minimize the
energy... if it blows up, you should start with an even smaller density.
• gmx grompp -f min.mdp -c box_noeq.gro -p topol.top
• gmx mdrun
• mv confout.gro box_eq.gro

I added a last line to change the name of the output *.gro file so that it says it is the equilibrated
box.
O.K., let's assume you were able to minimize. Now you increase the density and minimize again....
and repeat until you arrive to the desired density.
• gmx editconf -f box_eq.gro -density 750 -o box_noeq.gro
• gmx grompp -f min.mdp -c box_noeq.gro -p topol.top
• gmx mdrun
• mv confout.gro box_eq.gro

You must repeat these lines until you have converged... and that's all (if you manage at the very first
time, the you are really very lucky or very good!!!).
It is maybe better to do this in an automatic way using a bash file like this one.
By now you shoud have produced:
• A confout.gro file with the final configuration
• A traj.trr with the trajectory of your molecules
• An ener.edr with the energy

Let's have a look at these files:

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