[gmx-users] Fwd: Problem in applying walls in the z direction

[Stephen Chan]

I notice that they are the hydrogen atoms of the same water molecule and 
they may have been split by the PBC in the previous step. I'll prepare 
the gro again. Thanks for your help.

Cheers

On 07/02/16 22:23, Justin Lemkul wrote:
>
>
> On 7/2/16 4:20 PM, Stephen Chan wrote:
>> Hi Justin,
>>
>> Just above the fatal error message, there is some additional 
>> information:
>>
>> Initializing Domain Decomposition on 112 ranks
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>     two-body bonded interactions: 10.867 nm, Exclusion, atoms 30544 
>> 30545
>>   multi-body bonded interactions: 0.488 nm, CMAP Dih., atoms 1075 1091
>> Minimum cell size due to bonded interactions: 11.954 nm
>> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 
>> 0.222 nm
>> Estimated maximum distance required for P-LINCS: 0.222 nm
>> Guess for relative PME load: 0.23
>> Will use 84 particle-particle and 28 PME only ranks
>> This is a guess, check the performance at the end of the log file
>> Using 28 separate PME ranks, as guessed by mdrun
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 84 cells with a minimum initial size of 
>> 14.942 nm
>> The maximum allowed number of cells is: X 0 Y 0 Z 2
>>
>> Do I need to adjust other parameters in the mdp accordingly??
>>
>
> No, you need to investigate this:
>
>   two-body bonded interactions: 10.867 nm, Exclusion, atoms 30544 30545
>
> Bonded interactions are normally within 1.5 nm or so.  A distance this 
> large suggests something bizarre going on in your topology. Figure out 
> what these atoms are and what is going on with them.
>
> -Justin
>