Virtual Sites

[phthalimid]

I tried to use a virtual site but ran into difficulties. In the .itp file, I labelled the site with a 'v' in front of the type:

[...]
[ moleculetype ]
; molname nrexcl
FLN 1

[ atoms ]
; id type resnr residue atom cgnr charge mass
1 TC5 0 FLN B0 1 0.00000 49.5
2 TC5 0 FLN B1 2 0.00000 49.5
3 vSC5e 0 FLN B2 3 0.00000 0
4 TC5 0 FLN B3 4 0.00000 49.5
5 TC5 0 FLN B4 5 0.00000 49.5
6 TN6a 0 FLN B5 6 0.00000 36

[bonds]
; i j funct length
6 3 1 0.225 25000
[...]

Then, I removed the bead from the .ndx file, because Swarm-CG asked me to. The, it recognised the virtual site, but crashed when calling "map_aa2cg_traj":

Command line: /home/nannthom/anaconda3/envs/swarmcg/bin/scg_evaluate -aa_tpr swarmCG_data/aa_topol.tpr -aa_traj swarmCG_data/aa_traj.xtc -cg_map swarmCG_data/cg_map.ndx -cg_itp swarmCG_data/cg_model.itp -cg_tpr swarmCG_data/cg_topol.tpr -cg_traj swarmCG_data/cg_traj.xtc

+---------------------------------------------------------------------------------------------+
| PRE-PROCESSING |
+---------------------------------------------------------------------------------------------+

Reading Coarse-Grained (CG) ITP file
Found 5 beads
Found 1 virtual sites
Found 4 constraints groups
Found 1 bonds groups
Found 0 angles groups
Found 2 dihedrals groups

Reading All Atom (AA) trajectory
Found 5001 frames

Mapping the trajectory from AA to CG representation
Interpretation: Center of Mass (COM)
Traceback (most recent call last):
File "/home/nannthom/anaconda3/envs/swarmcg/bin/scg_evaluate", line 8, in
sys.exit(main())
File "/home/nannthom/anaconda3/envs/swarmcg/lib/python3.9/site-packages/swarmcg/evaluate_model.py", line 237, in main
run(ns)
File "/home/nannthom/anaconda3/envs/swarmcg/lib/python3.9/site-packages/swarmcg/evaluate_model.py", line 125, in run
scg.map_aa2cg_traj(ns)
File "/home/nannthom/anaconda3/envs/swarmcg/lib/python3.9/site-packages/swarmcg/swarmCG.py", line 1357, in map_aa2cg_traj
traj[ts.frame] = ns.mda_beads_atom_grps[bead_id].center(
KeyError: 5

Looks like a bug to me.