GROMACS modification: Yes/No
I have a system with 4500 solvent (spce water model) and a solute. I want to have a shell with a radius of 1 nm around the solute and obtain only the energy interaction of the components in this shell with the solute. Would you please help me? which command can do this? Is this possible in Gromacs?
This would require a dynamic selection, not a static index group, and that is not something
mdrun can automatically handle. The only solution here would be to process each frame individually, using
gmx select to create an index file for a frame that includes the groups of interest, then using
mdrun -rerun with that new index file and the frame. That is very cumbersome, but could be done. Note that the interaction energy value may or may not mean anything, depending on the force field you used, and will be dependent on the number of molecules that satisfy the radius criterion, so the values may change dramatically depending on if there are a different number of molecules in the groups in each frame.
I didn’t understand what must I do, how can I insert the radius using
gmx select or mdrun -rerun ? which flags must be used in both commands?
it’s necessary to say that, I want to have a sphere with a radius of 1 nm from COM of solute and calculate all the interactions inside this sphere. I’m using of GROMOS 54A7 Obtained from ATB server.
Please refer to
gmx help selections for syntax in using
gmx select and selections in GROMACS, in general. Interaction energy is computed in
energygrps in the
.mdp file and subsequently the
.tpr file. Your case requires that the selection (index group) be made for every frame, since the species that satisfy the COM distance criterion will be different.