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

[RJ]

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:
topol.tpr






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. 

-Justin