Hello.

You have to define energy groups within the .mdp file.

energygrps = Protein SOL

Ricardo

Hello.

You have to define energy groups within the .mdp file.

energygrps = Protein SOL

Ricardo

Thanks for your help.

It seems working.

One more question, when I use g_energy to export the potential, there are Coul-SR and Coul-14, what is the difference between them?

Can we also get the bonding energy between the peptide?

I am very new in Gromacs, your anwser really help a lot.

Hello.

Coul-SR is the short-range electrostatic (coulombic) interactions, and are far more used to assess the system's equilibration along the simulation run. Coul-14 are long range coulombic interactions and will depend on your cut-off radius.

For bonding energy, you first have to create an index file with the residues that you are interested. Then, you can use g_hbond for hydrogen bonds. For non-bonded GROMACS doesn't have a tool that allows any determination.

Nonetheless, this is all very well explained in the GROMACS manual. Print it and have it as your bed-side reading. Your're gonna need it! :-)

Any thing, just ask.

Ricardo

Thanks for your suggestion, more bed-side reading.

Something are confusing me, correct me if I am wrong.

I have export the LJ-SR and LJ-14 for protein-protein interaction. The value is about -200kJ/mol for LJ-SR and 300kJ/mol for LJ-14.

I know the Lennard-Jone potential is only positive at short range, and negative at long range, but what I saw is reverse: negative at short range (LJ-SR:-200) and positive at long range (LJ-14:300).

I am very new in this field, maybe I am misunderstanding something or maybe the formula for Lennard-Jone potential is different for long range and short range.