single-bead residue + VS gives incorrect volume

[fgrunewald]

Describe the bug The volume of a single bead residue with another VS on top is incorrectly set to zero instead of the bead-size. The cause is the estimate of the volume filters out all volume contributions directly on top of the center of geometry, in order to avoid the unit vector to become undefined.

Command line arguments

polyply gen_coords -p test.top -o test.gro -name test -box 10 10 10

Expected behavior Generates the coordinates without getting stuck.

Additional Files test-itp file

[ moleculetype ]
GG 1
[ atoms ]
1 N1 1 PEO BB  1 0.0 
2 N2 2 PEO BB  2 0.0 
3 VS  1 PEO OR 3 0.0 
4 VS  2 PEO OR 4 0.0 
[ bonds ]
1 2 1 0.350 4000
[ virtual_sitesn ]
3 1 1
4 1 2

and any Martini3 topology file.

Workaround

provide a build file with the residue volume like so:

[ volumes ]
PEO 0.47