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

Makoto Yoneya makoto-yoneya at aist.go.jp
Mon Aug 25 12:04:49 CEST 2008

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
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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