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.) 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 (127.0.0.1) 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 advance.
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