MD: Setup MD in solvent

Introduction

A pre-equilibrated box of solvent molecules is required.

Setup of the environment

Open a terminal in the server (this instruction depend on the configuration of the server)

If a setup file is present it is possible to use the instruction source

In this case the setup file is located in the HOME directory and is named gromacs_setup.source

Preparation of MD files

Mandatory files that must be present in the directory

• the original topological file prepared before the setup of other MDs run
• no information about solvent should be present
• file pdb of the solute
• file pdb of the solvent
• topological file (.itp) of the solvent molecules

Create the gro files with information about the box dimensions

Then solvate the solute (here a box of chloroform was used)

Now, modify the topological file to include solvent information

• Add after #include "amber99sb.ff/forcefield.itp" the field [ Atomtypes]

[ atomtypes ]
; name   mass       charge   ptype   sigma(nm)     epsilon (kJ/mol)
 cl      35.500000  -0.30270     A   3.47094e-01   1.10876e+00
 h3       1.000000   0.30060     A   2.11499e-01   6.56888e-02
 c3      12.000000   0.00070     A   3.39967e-01   4.57730e-01

• Add before [ system ] the following lines

; Include solvent topoly
#include "CHL.itp"

• Finally, in the [ molecules ] section add the name and the number of the solvent molecules (information that can be obtained from the file gro with the solvatate solute

[ molecules ]
; Compound        #mols
Protein             1
CHL               226

In the topology file the order of the fields is important to avoid errors.

Now,  try that all is ok using the file minim.mdp

gmx grompp -f minim.mdp -c mv1_model1_solv.gro -p topol_cyc.top -o em