[gmx-users] Re: Replica Exchange MD using Gromacs

[Mark Abraham]

On 25/05/2011 12:50 AM, jen.johnston at lycos.com wrote:
> Hi,
> I have exactly the same problem as is described below. I am using 
> version 4.5.4 with the Plumed metadynamics plugin.
>
> I was wondering if there was any update on dealing with the bug?

The original poster never filed a bug request, so there was never 
anything to debug.

I can do so if you have a reproducible non-Plumed case where gmxcheck on 
the .tpr files (and any .cpt files input with mdrun -cpi) reveals no 
differences in things like init_step and nsteps, and mdrun thinks there 
is a mismatch. If so, please file a Redmine request. 
http://redmine.gromacs.org

Mark

> Many thanks,
> Jen
>
> Today's Topics:
>
>
>     1. Re: Replica Exchange MD using Gromacs (Mark Abraham)
>     2. Re: FW: protein split over boundary (ravi sharma)
>     3. Re: FW: protein split over boundary (Justin A. Lemkul)
>
>
>     ----------------------------------------------------------------------
>
>     Message: 1
>     Date: Fri, 01 Apr 2011 22:30:56 +1100
>     From: Mark Abraham <Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>>
>     Subject: Re: [gmx-users] Replica Exchange MD using Gromacs
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4D95B770.1070805 at anu.edu.au
>     <mailto:4D95B770.1070805 at anu.edu.au>>
>     Content-Type: text/plain; charset="iso-8859-1"
>
>     On 1/04/2011 6:52 PM, bsmith wrote:
>     > On 01/04/2011, at 6:29 PM, Mark Abraham wrote:
>     >
>     >> On 1/04/2011 6:03 PM, Ruchi Gupta wrote:
>     >>> Dear gmx-users,
>     >>>
>     >>> I am facing some problems while running replica exchange MD using
>     >>> Gromacs.
>     >>>
>     >>> Few seconds after the job submission it ends with the following
>     >>> error message:
>     >>>
>     >>> "
>     >>> Initializing Replica Exchange
>     >>>
>     >>> Repl There are 6 replicas:
>     >>> Multi-checking the number of atoms ... OK
>     >>> Multi-checking the integrator ... OK
>     >>> Multi-checking init_step+nsteps ...
>     >>> init_step+nsteps is not equal for all subsystems
>     >>> subsystem 0: 0
>     >>>
>     >>> subsystem 1: 50000
>     >>> subsystem 2: 0
>     >>> subsystem 3: 50000
>     >>> subsystem 4: 0
>     >>> subsystem 5: 50000
>     >>>
>     >>> -------------------------------------------------------
>     >>> Program mdrun, VERSION 4.5.4
>     >>> Source code file: main.c, line: 249
>     >>>
>     >>>
>     >>> Fatal error:
>     >>> The 6 subsystems are not compatible
>     >>>
>     >>> For more information and tips for troubleshooting, please
>     check the
>     >>> GROMACS
>     >>> website athttp://www.gromacs.org/Documentation/Errors
>     >>>
>     >>> -------------------------------------------------------
>     >>>
>     >>> "
>     >>>
>     >>> I am using a "single .gro file" and "6 different md.mdp" files
>     (at 6
>     >>> different temperatures) for generating "6 .tpr files",
>     respectively.
>     >>> But the simulation doesn't work.
>     >>>
>     >>>
>     >>> I have compared the ".tpr files" using "gmxdump" and "gmxcheck"
>     >>> Gromacs commands and they seem fine with respect to nsteps and
>     >>> init_step information.
>     >>
>     >> So, to be clear, gmxcheck says that for no pair of .tprs does
>     >> init_step or nsteps differ...
>     >>
>     >> What is your mdrun command line? Are you using checkpoint files?
>     >>
>     >> Mark
>     >> --
>     >> gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     >> <mailto:gmx-users at gromacs.org>
>     >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>     >> Please search the archive at
>     >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     >> Please don't post (un)subscribe requests to the list. Use the www
>     >> interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>     >
>     > 1) Comparison of the .tpr files using gmxdump reveals no
>     differences
>     > but for the temperatures and the velocities in each i.e.
>     init_step and
>     > nsteps have the same values (0 and 50000, respectively) in all
>     files.
>     >
>     > 2) We have tried running mdrun without checkpointing (-cpt -1) and
>     > with checkpointing with no change in the outcome.
>
>     That sounds like a bug. Please create a new Redmine issue here
>     http://redmine.gromacs.org and attach your .tpr and .mdp files -
>     preferably in a compressed archive file. You should get the option to
>     assign it to me - please do.
>
>     Mark
>     -------------- next part --------------
>     An HTML attachment was scrubbed...
>     URL:
>     http://lists.gromacs.org/pipermail/gmx-users/attachments/20110401/471a7c08/attachment-0001.html
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110525/7ef41cb0/attachment.html>