Problem wtih funnel opes simulation

[ANTONIO LAUS]

Hi everyone,

I need help with a simulation involving the funnel. The error I'm encountering is the following:

```
PLUMED: ################################################################################
PLUMED:
PLUMED: (tools/Grid.cpp:168) PLMD::GridBase::index_t PLMD::GridBase::getIndex(const std::vector<unsigned int>&) const
PLUMED: Looking for a value outside the grid along the 0 dimension (arg name: fps.lp)
PLUMED:
PLUMED: The above exception was the direct cause of the following exception:
PLUMED:
PLUMED: (core/PlumedMain.cpp:980) void PLMD::PlumedMain::justCalculate()
PLUMED: An error happened while calculating funnel
PLUMED: ################################################################################
```

It seems to be caused by `fps.lp`, but when I check the COLVAR file, it does not appear to be out of bounds. Additionally, it seems that the `funnel.bias` is not being applied within the cylinder, as the value remains at 0.

I am attaching the `file.dat` and the final part of the COLVAR file at the time of the error:

Thank you in advance for your help!

[ANTONIO LAUS]

Hello everyone, I also attach the video.
It looks like a bug is like it doesn't feel the potential of the funnel

[Robert Coffman]

Antonio,

This can happen for several reasons that you may have found. However, one reason that I haven't seen elsewhere, is that the reference file shouldn't contain more than one chain. I found, by uncommenting a couple of the debug lines in FPS.cpp, I would get an erroneous output showing that the funnel needed to be moved a fair distance from where it started causing my ligand to now be outside the funnel. This is a feature used to keep the funnel aligned with your target protein. My particular problem was fixed when I chose one of the subunits to be written to my ref.pdb file and NOT both. I chose the subunit that contained my anchor atom.

Sincerely,

Robert