virtual: CENTER ATOMS=1
p2: PATH REFERENCE=all.pdb LAMBDA=69087    
p2b: PATH REFERENCE=all1.pdb LAMBDA=69087    
p3: PATHMSD REFERENCE=all.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5
PRINT ARG=p2.spath,p2.zpath,p3.sss,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
DUMPDERIVATIVES ARG=p2.spath,p2.zpath,p3.sss,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f
PRINT ARG=p2.spath,p2.zpath,p2b.spath,p2b.zpath FILE=colvarb FMT=%8.4f

# dummy action to activate the virtual atom every ten frames, as a check
p3b: PATHMSD REFERENCE=all1.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5
PRINT ARG=p3b.sss,p3b.zzz FILE=colvarc STRIDE=500 FMT=%8.4f
