[gmx-users] Generate many random configurations

Justin Lemkul jalemkul at vt.edu
Thu Mar 6 20:03:25 CET 2014

On 3/6/14, 9:50 AM, rankinb wrote:
> 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.

Are you calculating the g(r) for a single configuration, or over a trajectory?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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