[gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

[ZHANG Cheng]

My coarse-grained system has 10 proteins, each has 442 residues. After a period of time, those proteins aggregated. I want to use "gmx distance" to know which residues most likely to involve contact with other proteins.


I prepared a index.ndx file, in which there are 442*442*(9+8+7 ... + 1) = 8791380 pairs of atom indices. But these indices are extremely too long for Gromacs to handle at a time. So I have to split it into shorter pieces.


But is there a more efficient way to achieve this?


Thank you!


Cheng