[gmx-users] Re;calculating interaction energies of dimers and ligand

RJ rajiv at kaist.ac.kr
Mon Feb 16 06:03:23 CET 2015

Dear Justin,

I notice that -rerun option in mdrun.

As per your suggestion, i have made a tpr file using energyrps in md.mdp file as like this 

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -o check.tpr

and tried to use mdrun -reun 

gmx mdrun -rerun check

but end up with 

Can not open file:

Dear Justin,

I already ran 10 ns without mentioned the energyrps. Now I have added the energyrps in md.mdp file. Should i need to rerun 10 ns again to get the interaction energies?

what does mdrun -rerun ? 
On 2/13/15 7:07 AM, RJ wrote: 
> Dear all, 
> I need to calculate the interaction energy (Column SR & LJ SR) of chain A with chain B. 
> Should I need to select the specific interacting residues to between chain A and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line but there are index.ndx option to indicate the group of residues so? 

To get this information printed to the .edr file, you need to do your run with 
correct energygrps defined. If you didn't do that, create a .tpr file that 
specifies these groups and re-calculate energies with mdrun -rerun. 

> Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)? 

Just convert after the fact in the text file or plotting software. The time 
unit is always ps in .edr files. 


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