Hi Romnik, One simple thing you could try is increase the min distance in the options file and see if that helps.
There could be other issues depending upon how you coarse-grain the water molecules and how you assign the charges in the CG topology. If you could please send us the input files, I would be able to better answer this issue. Thanks, Sikandar On Wed, Mar 22, 2017 at 2:30 PM, Christoph Junghans <[email protected]> wrote: > 2017-03-22 5:55 GMT-06:00 Rom <[email protected]>: > > Hi all :) > > > > I am working on a system where I have a large charged dye molecule, a > > charged counterion, and water as the solvent. > > > > The atomistic simulations are good, and yet when i force match the > > interactions, any interaction with the counterion (counterion-counterion, > > dye-counterion etc) all show a force profile of peaks and wells at around > > 10^13 and 10^-13! > > I thought maybe it was the -rerun part, so I deleted all the charges in > my > > topology before re-running, since i thought it was the charge that was an > > issue, and yet it is still doing this! > > > > Does anyone know what the problem is? Is there a certain way to deal with > > charged molecules when force matching? > That is more a question for Sikandar.... > > > > > Many thanks! > > Romnik > > > > p.s. if you need to look at any files, just let me know so I can attach > them > > > > -- > > 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. > > 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. > For more options, visit https://groups.google.com/d/optout. > -- 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. For more options, visit https://groups.google.com/d/optout.
