IBI bonded potentials

[CHRISTINA-ANNA GATSIOU]

Hi, 

I have been trying to perform IBI on a PEG oligomer (6 monomers). I have used only one bead type for each monomer. This degrees of freedom of my cg system are one bond type , one angle type, one dihedral type and one nonbonded interaction. I have generated a sufficiently long trajectory in order to obtain smooth distributions. However, my iterations always stop at the 1st step, with gromacs failing after a bond gets out of range. The tabulated bond potential generated by VOTCA seems very shallow compared to what I would expect from the inversion of the target distribution. Is there a possibility that something is not computed properly. Please find attached the corresponding plots. (The units in the plots correspond to x [nm]  y [ kJ/mol]). Any help would be much appreciated.

Best regards, 

Christianna 

[Christoph Junghans]

Sometimes setting up bonded interaction is tricky as you need to get
the range where initial inversion is performed right.
If you can make a better initial guess for the potential than what
VOTCA calculates (.pot.new in step_000), you can provide that as
<name>.pot.in in the main directory and VOTCA will use it instead of
the BI inverted PMF and then perform IBI on top of that.

Christoph
>
> Best regards,
> Christianna
>
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Christoph Junghans
Web: http://www.compphys.de

[Joshua Brown]

Hi Christianna,

Are you using lammps input files, if so what units are you using?