[gmx-users] Replica Exchange MD using Gromacs

[bsmith]

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
> -- 
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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.

Regards

Brian

Dr Brian J Smith
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Victoria 3052, Australia
Ph: +61 (0)3 9345 2687 Fax: +61 (0)3 9345 2686
http://www.wehi.edu.au/brian_smith





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