[gmx-users] Walls & user defined potential

Bert bert.ustc at gmail.com
Tue Oct 21 23:55:16 CEST 2008

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

; Number of walls, type, atom types, densities and box-z scale factor for
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.)

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

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.

If you have any suggestions, that would be much appreciated. Thanks in
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081022/720770ac/attachment.html>

More information about the gromacs.org_gmx-users mailing list