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. Thank you! ------------------ Original ------------------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Feb 19, 2019 05:13 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@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? Thank you! Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
