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