4. Position-restrained equilibration¶
We first perform a short MD simulation with harmonic position restraints on the heavy protein atoms. This allows the solvent to equilibrate around the protein without disturbing the protein structure. In addition, we use “weak coupling” temperature and pressure coupling algorithms to obtain the desired temperatue, \(T = 300\) K, and pressure, \(P = 1\) bar.
4.1. Set up and generate the run file¶
We must first tell Gromacs how to perform our equilibration run
in the same way that we did for the energy minimization step.
This step requires the
top/protein_posres.itp file with the
default value for the harmonic force constants of 1000
kJ mol-1 nm-2. The position restraints are switched on by setting the
-DPOSRES flag in the
posres.mdp file (see mdp options).
Create the run input (TPR) file, using the energy minimized system as the starting structure:
cd ../posres cp ../templates/posres.mdp . gmx grompp -f posres.mdp -o posres.tpr -p ../top/4ake.top -c ../emin/em.pdb -maxwarn 2
The mdp file contains cut-off settings that approximate the native CHARMM values (in the CHARMM program).
Weak (Berendsen) coupling is used for both temperature and pressure to
quickly equilibrate. The protein and the solvent (water and ions) are
coupled as separate groups. Gromacs provides a range of groups
make_ndx -f TPR to see them) and we use
non-Protein (these particularly groups
work since roughly Gromacs 4.5.3). If the standard groups do not work
then you will have to create the groups yourself using
-f TPR -o md.ndx (which would save them in a file
supply it to
gmx grompp -n md.ndx.
4.2. Perform equilibration¶
Run the position restraints equilibration simulation:
gmx mdrun -v -stepout 10 -s posres.tpr -deffnm posres -c posres.pdb
(If this is too slow on your workstation, submit to saguaro using 8 cores.)
Here the runtime of 10 ps is too short for real production use; typically 1 to 5 ns are used.
Generate a centered trajectory in the primary unitcell
In order to visually check your system, first create trajectory with all
molecules in the primary unitcell (
-ur compact; see also below the
more extensive notes on trajectory-visualization):
echo "System" | gmx trjconv -ur compact -s posres.tpr -f posres.xtc -pbc mol -o posres_ur.xtc
If you don’t have a vmd command available on the command
line then launch VMD, load the
( ), highlight your molecule 1
(“em.pdb”) and load the
posres/posres_ur.xtc trajectory into your
molecule 1”, . You
should see that the first frame (from the energy minimization) looks
as if the water is in a distorted box shape whereas all further frames
show a roughly spherical unit cell (the rhombic dodecahedron).