[gmx-users] Problem with binding energy
btam125 at hotmail.co.uk
Thu Aug 18 13:34:49 CEST 2016
I have a problem with calculation with binding energy with using gromacs. My calculation is the binding of solvent onto a crystal.
The steps I took to calculate binding energy is like this:
1) Energy minimised my crystal system with the solvent.
2) Calculated the energy of the crystal-solvent system by using gmx energy - total energy is selected (this is done by using only time 0 energy step shown from energy.xvg)
3) I extract the co-ordinate of the solvent from the minimised system and calculate the energy by using gmx energy - total energy is selected (this is done by using only time step 0 energy shown from energy.xvg)
4)Extract the co-ordinate of the crystal from the minimised system and calculate the energy similar to the previous step.
5) Energy of the Crystalsolvent system - energy of the crystal - energy of the solvent = binding energy.
The problem I have is, after the calculation I proposed, the binding shown as -6000 kJ/mol. With other software, the binding energy is calculated as -250 kJ/mol.
I have triple check my molecules connectivity and the charges and the force field. Everything seems to be reasonable. Henceforth, what can caused the extremely high binding energy?
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