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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="EC_stopSpelling">Date: Wed, 22 Oct 2008 05:55:16 +0800<br>From: bert.ustc@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Walls & user defined potential<br><br><div>Hi gmx-users and developers,</div>
<div> </div>
<div>I met a strange error when using wall function combined with user defined potential. Following is a part of the mdp:</div>
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<div>------------------------------------------------------------------------</div>
<div>vdw-type = user</div>
<div>energygrps = Surf SOL</div>
<div> </div>
<div>; WALLS <br>; Number of walls, type, atom types, densities and box-z scale factor for Ewald<br>nwall = 2<br>wall_type = table<br>wall_r_linpot = -1<br>wall_atomtype = W1 W2<br>
wall_density = 1.5 1.5<br>wall_ewald_zfac = 2</div>
<div>energygrp_table = Surf wall0 Surf wall1 SOL wall0 SOL wall1 </div>
<div>table-extension = 1.0</div>
<div>------------------------------------------------------------------------</div>
<div>1) With the command bellow,</div>
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<div>mdrun -table table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod</div>
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<div>A fatal error was generated: Library file table_Surf_wall0_Surf_wall0.xvg not found in current dir nor in default directories.</div>
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<div>Then I copy the table6-12.xvg from the top dir, rename it by table.xvg and add it in the command line,</div>
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<div>mdrun -table table6-12.xvg table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod</div>
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<div>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.)<br><br><br>This table should not be necessary.<br>I can see if I can modify the code such that it does not ask for this combination.<br><br></div>
<div>Note that you can use wall_type=table together will normal non-user vdw and Coulomb.<br><br><br><br></div>
<div>2) But when I make a parallel run, a crash was found: </div>
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<div>One of the processes started by mpirun has exited with a nonzero exit<br>code. This typically indicates that the process finished in error.<br>If your process did not finish in error, be sure to include a "return<br>
0" or "exit(0)" in your C code before exiting the application.</div>
<div>PID 5798 failed on node n0 (<a href="http://127.0.0.1" target="_blank">127.0.0.1</a>) due to signal 11.<br>-----------------------------------------------------------------------------<br>mpirun failed with exit status 11</div>
<div> <br><br>Can you send me the input for this (or file a bugzilla)?<br><br><br></div>
<div>3) Moreover, if table-extension set to 0.0, a fatal error was caught: <br>'An atom is beyond the wall: coordinates -5371173273600.000000 -20382570512384.000000 2778490208256.000000, distance -1.000000<br>You might want to use the mdp option wall_r_linpot'</div>
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<div>I have tested several values, crash is found only when this value is less than 0.2.</div>
<div><br><br>You should never set table-extension to 0.<br>You need a certain extension for charge group size and atom diffusion with nstlist steps.<br><br>Berk<br><br> </div>
<div>If you have any suggestions, that would be much appreciated. Thanks in<br>advance.<br></div>
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