[gmx-users] Simulation in clusters -reg
Hi gmx-users, I was trying to run my simulation in core cluster in my institute. It is showing the following error. But it works completely fine in my personal laptop. *the cluster error:-* MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. *the gromacs error:-* NOTE: Turning on dynamic load balancing A list of missing interactions: LJ-14 of479 missing 1 Molecule type 'Macromolecule' the first 10 missing interactions, except for exclusions: LJ-14 atoms 146 196 global 146 196 --- Program gmx mdrun, VERSION 5.1.2 Source code file: /root/gromacs-5.1.2/src/gromacs/domdec/domdec_topology.cpp, line: 435 Fatal error: 1 of the 2886 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.18407 nm) or the two-body cut-off distance (2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors thank you Meagha -- 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.
[gmx-users] wall time for every 1000 steps in simulation - reg
Hi, Is it possible to get actual wall time (0 to total time) every 1000 steps, instead of expected time? thanks Meagha -- 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.
Re: [gmx-users] dielectric constant -reg
hi mark, Same doubt in the following thread. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/106078.html with epsilon_-surface =0, simulation runs fine. The problem starts when I give it a value. My model has only protein and doesn't have anything other than that. Moreover, i have read the .mdp file, as you have mentioned in the previous threads. thank u Meagha On Mon, Sep 11, 2017 at 9:53 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Clearly the .mdp file changes you say you are making aren't showing up > later in wherever you are observing a 1.12, but we'll need to see a lot > more detail of your process - e.g. command lines with the file names - to > suggest what might be wrong. That means you need to be able to copy and > paste them from a terminal or script, or you won't generally be able to > reconcile what you think you did with what you actually did. > > Mark > > On Mon, Sep 11, 2017 at 9:51 AM Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Change the mdp file and use that file to make a new tpr file and that the > > file to run a simulation. > > > > Mark > > > > On Mon, 11 Sep 2017 08:21 Meagha ramana kumar <meag...@gmail.com> wrote: > > > >> Hi gmx-users, > >> > >> My problem may sound silly, but please help me with it. I know how to > >> change dielectric constant for simulation. Yes I have read all the > previous > >> thread reading this and no one provided straight answer to this. I am > using > >> PME. I tried changing all the epsilon values but nothing helped and I > get > >> 1.12. will be thankful , if you guys help me out. > >> > >> Thank you > >> Meagha > >> > >> > >> Sent from Mail for Windows 10 > >> > >> -- > >> 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. > >> > > > -- > 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. > -- 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.
[gmx-users] dielectric constant -reg
Hi gmx-users, My problem may sound silly, but please help me with it. I know how to change dielectric constant for simulation. Yes I have read all the previous thread reading this and no one provided straight answer to this. I am using PME. I tried changing all the epsilon values but nothing helped and I get 1.12. will be thankful , if you guys help me out. Thank you Meagha Sent from Mail for Windows 10 -- 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.
