[gmx-developers] walls and pbc setting in CVS code

[Berk Hess]

Hi,

The error message tells you (nearly) everything.
I guess you have a very small box and you have a high lincs_order and/or 
lincs_iter.
The error message tells you what to do.
Use -rcon
and/or decrease lincs_order and/or lincs_iter
or increase the box size.

Berk

Makoto Yoneya wrote:
> Dear GROMACS developers (Prof. Berk Hess):
>
> Here again about the same subject as I posted in the last month.
> I'd tried the following modification  (shown by Prof. Hess) of the CVS code.
>
>   
>>> In src/kernel/readir.c you have to comment out the line:
>>>  CHECK(ir->nwall && ir->ePBC!=epbcXY); and recompile grompp.
>>>       
>
> It works well and my original purpose (walls function with pbc=xyz.
> whereas, only pbc=xy was permitted with the falls function in the original
> code)
> would be accomplished by this modification (thanks a lot!).
>
> In the course of the trial, I found strange behaviors and I'll report
> for possible (?) bugfix.
> The code modification above was simply eliminates the checking
> on the pbc for the walls function.
> However if I'd tried walls function with pbc=xy, my parallel job (with 4
> nodes) was terminated with the following massage (this was same
> in the original code without the modification).
>
> --- begin the massage copy ---
> Initializing Domain Decomposition on 4 nodes
> Will not use dynamic load balancing
> Will sort the charge groups at every domain (re)decomposition
> Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 1.487 nm
> Estimated maximum distance required for LINCS: 1.487 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Optimizing the DD grid for 4 cells with a minimum initial size of 1.487 nm
> The maximum allowed number of cells is: X 4 Y 4 Z 1
>
> -------------------------------------------------------
> Program mdrun-mpi_d, VERSION 3.3.99_development_200800503
> Source code file: domdec_setup.c, line: 372
>    
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with the
> given box and a minimum cell size of 1.4875 nm
> Change the number of nodes or mdrun option -rcon or your LINCS settings
> Look in the log file for details on the domain decomposition
> ------end of the massage copy--------
>
> The corresponding parallel job with simply changing pbc=xyz 
> runs normally without any errors.
> With pbc=xy, single node job made no errors, then
> possibly the problem would be parallel decomposition
> with pbc=xy setting.
> Hope it helps.
>
> Thanks again the precious efforts of GROMACS developers.
>
> Makoto Yoneya, Dr.
> AIST, Japan
>
>   
>> -----Original Message-----
>> From: Makoto Yoneya [mailto:makoto-yoneya at aist.go.jp] 
>> Sent: Tuesday, July 22, 2008 11:17 AM
>> To: 'gmx-developers at gromacs.org'
>> Subject: walls and pbc setting in CVS code
>>
>> Dear Prof. Berk Hess and GROMACS developers:
>>
>> Thanks a lot for your reply and the precious info.
>> Sorry for my bad explanations.
>> I simply want to simulate the system with a water layer 
>> (modeled by a wall) and a monolayer on it.
>> So far the system can simulate with original CVS code.
>> However, I also want to add trans-monolayer constant vapor 
>> flow (in Z-direction) of water molecules from the water layer
>> (wall) to the system above.
>> I'll try the code modifications and check the result.
>>
>> Best regards,
>>
>> Makoto Yoneya, Dr.
>> AIST Japan
>>
>>     
>>> Hello,
>>>
>>> I don't understand exactly what you want to do.
>>> But if you are really convinced that it makes sense for your 
>>>       
>> research, 
>>     
>>> you can modify the code.
>>>
>>> In src/kernel/readir.c you have to comment out the line:
>>>  CHECK(ir->nwall && ir->ePBC!=epbcXY); and recompile grompp.
>>>
>>> Berk.
>>>
>>>
>>> Makoto Yoneya wrote:
>>> Dear GROMACS developers:
>>>
>>> I'd tried the walls function in the CVS code and found works well.
>>> In the current implementation, the walls function can only be used 
>>> with pbc=xy as in the online manual.
>>> However, I'd like to use the walls without the pbc=xy setting (i.e.
>>> the common 3-D pbc).
>>> I'm considering a Langmuir monolayer (monolayer on a water 
>>>       
>> layer) and 
>>     
>>> trans monolayer water (in Z-direction from the water
>>> layer) simulation.
>>> The water layer may be modeled with the wall function with the 9-3 
>>> potential.
>>> The trans monolayer water vapor flow (in Z-direction) may 
>>>       
>> be modeled 
>>     
>>> with specifying,
>>> energygrp_excl: VAPOR_WATER wall0
>>> and
>>> acc_grps: VAPOR_WATER
>>> accelerate: 0.0 0.0 0.5.
>>> So, the water molecules may flow periodically in Z-direction (then 
>>> requires 3-D pbc).
>>>
>>> If these may work, then please consider to work the walls function 
>>> even without pbc=xy.
>>>
>>> Thank you for advance.
>>>
>>> Makoto Yoneya, Dr.
>>> AIST, Japan
>>>
>>>
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