[gmx-users] Generate many random configurations

rankinb rankinb at purdue.edu
Thu Mar 6 15:51:06 CET 2014

Thanks for your reply and helpful suggestions Justin.  I have successfully
implemented the concatenation command (after generating the desired number
of configurations).  There is another detail with which I am having trouble. 
So, I actually want to generate configurations in which it is possible for
atoms to overlap, as in an ideal gas.  To do that, I set vdwd to 0.01 nm and
used atom names that are not contained in the vdwradii.dat file so that vdwd
will actually be used.  (Ideally, I want to use vdwd=0, but I receive the
error, "One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the cut-off."). 
Regardless, even when vdwd=0.01, the g(r) still equals 0 at distances <= 0.1
nm.  Do you have any ideas why this is the case?  I thought that the g(r)
would be equal to zero at distances <= 0.01 nm.

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