[gmx-users] Generate many random configurations
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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