Understanding energy minimization working and acceptable scores

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
I got the following
tatistics over 2636 steps [ 0.0000 through 2635.0000 ps ], 1 data sets
All statistics are over 2087 points (frames)

Energy Average Err.Est. RMSD Tot-Drift

Potential 7.15491e+07 7.7e+07 3.42742e+09 -4.59299e+08 (kJ/mol)

Is this value acceptable and can I proceed for further equilibration step. I am new to gromac I earlier run tutorial lysozyme in water and the energy minimization average was negative score. But here I use modelled protein for MD and I got positive average as indicated above.

Kindly guide me.

The protein has 11482 atoms
solvent molecules 94698
qtot -19

2

Hi Rhaul,

The absolute value of the potential energy is not very meaningful, I suggest you have a look at the change of the potential energy.

If you plot the energy values during your energy minimisation, you would expect a strong drop in energy from the be beginning and then some curve that levels off. That is usually an indication that things went right.

I notice, that you have a large negative charge in your system. Unless you have a very strong reason for this, I suggest you add ions to balance the charges, just as in the lyzosyme tutorial.