GROMACS version: No
GROMACS modification: No
Dear Justin and GROMACS buffs,
I am trying to obtain energetics contributions of the several parts implied in a protein system simulated but also the atom-pair contributions of each. Of course, I already obtained the individual total contributions for LJ, and Coul, I mean 1-4, SR, Coul-Recip (Long Range I mean) for the three pair-entities: Protein-Protein, Protein-nonProtein and nonProtein-nonProtein.
However, I would like also to break down the term Coul-recip associate to PME. I’ve read in the forum by Justin that this is not possible, is it still not possible?
On the other hand, I’ve obtained the following information from the grompp preprocessing in my system:
Generated 20910 of the 20910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17803 of the 20910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
Excluding 2 bonded neighbours molecule type ‘SOL’
Excluding 1 bonded neighbours molecule type ‘CL’
Making dummy/rest group for Acceleration containing 193475 elements
Making dummy/rest group for Freeze containing 193475 elements
Making dummy/rest group for VCM containing 193475 elements
Number of degrees of freedom in T-Coupling group Protein is 4273.97
Number of degrees of freedom in T-Coupling group non-Protein is 383544.03
One question is, if the 20910 non-bonded parameter combinations shown for my solvated protein system (1705 Protein atoms and 191770 non-Protein atoms) refer here just to those non-bonded pair interactions below the established cutoffs, I mean, if they are only Short Range Interactions, right? …otherwise I cannot understand why so few non-bonded pair-interactions obtained with such a large number of atoms.
And finally, can you please tell me if there is any relationship between the number of degrees of freedom in T-Coupling groups (Protein and nonProtein) and the PP and nPnP pair-interactions, respectively, in the whole system?
Appreciate a lot your Help!!!