[gmx-users] energy

mirko busato busato.mirko at yahoo.com
Fri May 9 12:31:01 CEST 2014

Dear Users,

In my experiment, one petide of troponin protein  and many copies of the same type of  monomer, itaconic acid,(negatively charged) are assembled in a virtual box. 

I would like to understand , if there is a method to calculate the interaction energy between the peptide and the monomers.

I am asking this because I would like to have an energetic value to determine the affinity of the itaconic acid monomer against the peptide.

My system is in vacuum and  NA sodium ions weren't added to neutralize the system, so my system is charged.

The force field used is CHARMM27  and I performed a minimization energy step  and an equilibration step. 

Could you help me?

Thank you very much,


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