[gmx-users] Walls & user defined potential

Berk Hess gmx3 at hotmail.com
Wed Oct 22 09:52:53 CEST 2008

Date: Wed, 22 Oct 2008 05:55:16 +0800
From: bert.ustc at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Walls & user defined potential

Hi gmx-users and developers,
I met a strange error when using wall function combined with user defined potential. Following is a part of the mdp:
vdw-type                 = user
energygrps              = Surf   SOL
; WALLS                
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall                      = 2
wall_type                = table
wall_r_linpot            = -1
wall_atomtype         = W1  W2

wall_density            = 1.5  1.5
wall_ewald_zfac       = 2
energygrp_table       = Surf  wall0  Surf  wall1  SOL  wall0  SOL  wall1 
table-extension        =  1.0
1) With the command bellow,
mdrun -table table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod
A fatal error was generated: Library file table_Surf_wall0_Surf_wall0.xvg not found in current dir nor in default directories.
Then I copy the table6-12.xvg from the top dir, rename it by table.xvg and add it in the command line,
mdrun -table table6-12.xvg table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod
Am I right? It seems to be ok now. BTW, only the parameters in the replusive colunm in table_SOL_wall1.xvg are none zero (when z>1, these values are aslo set to zero.)

This table should not be necessary.
I can see if I can modify the code such that it does not ask for this combination.

Note that you can use wall_type=table together will normal non-user vdw and Coulomb.

2) But when I make a parallel run, a crash was found: 
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return

0" or "exit(0)" in your C code before exiting the application.
PID 5798 failed on node n0 ( due to signal 11.
mpirun failed with exit status 11

Can you send me the input for this (or file a bugzilla)?

3) Moreover, if table-extension set to 0.0, a fatal error was caught: 
'An atom is beyond the wall: coordinates -5371173273600.000000 -20382570512384.000000 2778490208256.000000, distance -1.000000
You might want to use the mdp option wall_r_linpot'

I have tested several values, crash is found only when this value is less than 0.2.

You should never set table-extension to 0.
You need a certain extension for charge group size and atom diffusion with nstlist steps.


If you have any suggestions, that would be much appreciated. Thanks in

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