[gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?
272699575 at qq.com
Tue Feb 19 13:28:29 CET 2019
Can I also ask, I am running it on high performance computer (HPC). So whether the cpu (-pe mpi 12) or memory (-l mem=2G) would influence the capability to handle a very long index file?
When the job is submitted, longer queue time will be required if requesting more resources. So I want to optimise the cpu and memory with the least queue time.
------------------ Original ------------------
From: "ZHANG Cheng"<272699575 at qq.com>;
Date: Tue, Feb 19, 2019 05:13 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
Subject: Is there a more efficient way to calculate the "gmx distance" with a very long index?
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?
More information about the gromacs.org_gmx-users