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

ZHANG Cheng 272699575 at qq.com
Mon Feb 18 22:14:48 CET 2019

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!


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