On 25/05/2011 12:50 AM, [email protected] 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 <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] Replica Exchange MD using Gromacs
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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 [email protected]
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>
> 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
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