Thanks guys! I tried using a larger minimum on many different mapping systems etc, even completely different simulations, and it still has the same issue.
I have attached a compressed file with my .xml mapping files, where str.xml = dye structure cou.xml = counterion sol.xml = water solvent index_62_5.ndx = index file for when i perform a rerun topology file I use for my rerun, along with the .itp file for each. On Wednesday, 22 March 2017 11:55:15 UTC, Rom wrote: > > 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? > > 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.
input_compress.tar.gz
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