You don't need g_enemat. If you use correct energygrps, the LJ and Coulombic terms are written to the .edr file and you can extract them with g_energy.

Note, though, that this quantity is not a "binding energy" - it is an interaction energy, and it may or may not yield a physically useful quantity.

You should have done it before running your simulation. In the *.mdp file, write

energygrps               =  group1 group2 group3 ..

(for example group1 can be define as the name of your Ligand in the *.ndx file: See also Gromacs website and search for energygrps for more details.)

and then run you simulation. After that in *.edr output you can find different interaction energy for each group.

You can rerun you simulation for short time (like 50ns) and see if the energy data have equilibrated (I assume your system has equilibrated). You can use g_analyze for making block errors and see if a short simulation can give you enough sampling.

However, for finding correct and useful free energy profile you need to perform PMF which is expensive and much more difficult.

thanks dear Weria

I think if generate a suitable *.dat file it will done ? what is your idea about it? 

To be Honest I do not know, what do you exactly mean by *.dat file. What do you want to do with this *.dat file? can you explain more.

Dear Weria 

thanks for your attention

I mea was can i use g_enemat? 

g_enemat extracts an energy matrix from the energy file (-f). With -groups (groups.dat as input file) a file must be supplied with on each line a group of atoms to be used. For these groups matrix of interaction energies will be extracted from the energy file by looking for energy groups with names corresponding to pairs of groups of atoms, e.g. if your -groups file contains:

2

Protein

SOL

You don't need g_enemat. If you use correct energygrps, the LJ and Coulombic terms are written to the .edr file and you can extract them with g_energy.

Note, though, that this quantity is not a "binding energy" - it is an interaction energy, and it may or may not yield a physically useful quantity.

In order to use g_enemat, you should first have done what I had told you. you should run the simulation with energygrps = group1 group2 group3in the *.mdp file. 

But if you have done this, you can use either g_enemat or g_energy. 

thanks deers

In addition to what correctly Justin said, g_energy will give you back the potential energy which is not the binding energy. To calculate the contribution of a particular residue to the binding free energy you have to exploit different approaches, going from accurate theories (i.e. TI, FEP) to less accurate theories (i.e. MM/PBSA MM/GBSA). In first approximation you can try the Computational Alanine Scanning (CAS), by which you mutate your residue in Alanine. In few words, you can run MM/PBSA on the wild system and the on the Alanine mutated one. The DDG = DG[wild] - DG[mutate] should give you the contribution of your residue in binding your ligand. For more information refers to this publications:

http://www.ncbi.nlm.nih.gov/pubmed/11457384

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046902

http://www.sciencedirect.com/science/article/pii/S0010465514003154

HTH

Best

thanks dear Andrea

Hello,

you can use g_mmpbsa for such calculations! :-)

Hello Justin Lemkul,

I also tried to use this method to do the energy decomposition analysis to explore the electrostatic interaction and the vdW interaction between to residues(explicitly solvent model). But I found that the electrostatic interaction between the positive charge residue and negative charge residue is so weak. I also calculated it by using the QM theory(PCM solvent model), and the result from the QM is quite strong. I'm confusing about why the electrostatic interaction is so weak in the GROMACS calculation, does it include the solvent effect, and does this interaction is affected by the PME? Would you give me some advice?

Best wishes,

Feng

Feng Yin interaction energies are a direct result of Coulomb's equation for charge-charge interactions. Force fields are generally not parametrized in such a way that examining LJ or electrostatic interaction energies individually is useful (or physically meaningful) in any way. Total interaction energy may be useful if parametrized against QM data (e.g. CHARMM and OPLS).

Do you mean that should I compare the QM total energy which includes the solvent effect with the total energy for the force field result? But should I also need to add the FF solvent total energy for the MM results also? I compared the MM electrostatic interaction with QM electrostatic interaction(I got this by using the PIEDA method), and vdW-MM with vdW-QM, and also can compare the total energy excluded the solvent effect between them. In this way, the QM-total energy (without the solvent energy) still much higher than the FF-total energy(without the solvent energy), but once I add the solvent effect to the QM result the total energy between the QM and FF does not have so much high difference. If the FF-electrostatic interaction is not affected by the solvent, which kind of reason produces this result?

Best wishes,

Feng

You can use G_mmpbsa. https://rashmikumari.github.io/g_mmpbsa/