On Sun, May 12, 2019 at 12:53 PM CHRISTINA-ANNA GATSIOU <[email protected]> wrote: > > 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.
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 > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/98a23e2e-b157-4ff0-a811-a3ae896c0c43%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7geENtyV3LC%2B9geMKe7w__V80B%3D6d%2BC3Xie1KxWt%2BpGA%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
