<pre>Hi all,<br><br>I have one question: when I use the "genbox -nmol 300 -ci a.gro -cp b.gro"<br>to insert a.gro into b.gro, for some system it gives good results, while not for others.<br>On the other hand, the -vdwd opinion seems not work. I looked at the code of gmx_genbox.c, but didn't find the reason.
<br><br>From the google, I found the following. The problem is the same as mine. Who has good suggestions?<br><br>Thanks in advance!<br><br>=======================================================================================
<br><a href="http://www.gromacs.org/pipermail/gmx-users/2004-August/011926.html">http://www.gromacs.org/pipermail/gmx-users/2004-August/011926.html</a><br>><i>The resulting output contains atoms which are too close. The distance
<br></i>><i>between the atoms is sometimes<br></i>><i>as small as 0.01 nm which is smaller than the vanderwaals radii from the <br></i>><i>database vdwradii.dat . Not<br></i>><i>surprisingly, therefore I get errors when I run energy minimization or mdrun.
<br></i>><i> The output keeps repeating the message "tested 0 pairs, removed 0 atoms <br></i>><i> " as I quote below. I would<br></i>><i>greatly appreciate if somebody could guide me how to use genbox properly.
<br></i><br>genbox isn't that good at randomly placing molecules within a box in cases <br>like this (are some emails in the archive on this). It needs a bit of <br>work. I use an in house program to do it, works out much better. Although
<br>I don't have it to give out to anyone, since it is part of a much larger <br>package that does a lot of other things and isn't mine to make available.</pre>