[gmx-users] Cohesive energies of Polymer Materials

wuxiao xiaowu759 at hotmail.com
Mon Jul 26 02:36:04 CEST 2010

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.

  xiaowu759 at hotmail.com
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