[gmx-users] Setting rcon according to system

Mark Abraham mark.j.abraham at gmail.com
Wed Nov 14 05:25:49 CET 2018


Possibly. It would be simpler to use fewer processors, such that the
domains can be larger.

What does mdrun think it needs for -rcon?


On Tue, Nov 13, 2018 at 7:06 AM Sergio Perez <sperezconesa at gmail.com> wrote:

> Dear gmx comunity,
> I have been running my system without any problems with 100 processors. But
> I decided to make some of the bonds of my main molecule constrains. My
> molecule is not an extended chain, it is a molecular hydrated ion, in
> particular the uranyl cation with 5 water molecules forming a pentagonal by
> bipyramid. At this point I get a domain decomposition error and I would
> like to reduce rcon in order to run with 100 processors. Since I know that
> by the shape of my molecule, two atoms connected by several constraints
> will never be further appart than 0.6nm, can I use this safely for -rcon?
> Thank you very much!
> Best regards,
> Sergio Pérez-Conesa
> --
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list