Dear gmx users,
I am performing one MD simulation of a polymer system using GROMACS-4.0.7. I
want to calculate the cohesive energy. According to the definition, cohesive
energy can be calculated the difference in energy between the model system with
and without pbc. I must perform the two separate simulations on the two
systems? Or more convenient, is the procedure below true?
1. to perform MD simulation (pbc = yes) on the model system with system and
to calculate the energies (old energies)
2. to edit the mdp file line: pbc = no, and to make another tpr file (new tpr
file) using this mdp file
3. to run mdrun -return using the old trr file and the new tpr file as the
inputs to calculate the energies (new energies)
4. to calculate the difference between the old and the new energies
please give me some hints.
Best regards,
Chaofu Wu, Dr.
[email protected]
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