Hi Romnik, As you know, force-matching tries to match the total force on the CG beads from CG force field with that from the reference atomistic simulations.
In your CG system, there are two components of the CG force field, first from the electrostatic interactions due to charges on the counterion and dye molecule and second from the vdW CG potentials. Therefore, in force-matching the objective is to force from electrostatics with CG topology + force from CG vdW potentials = total force from reference atomistic simulations. Since, csg_fmatch optimizes only the vdW component of the CG potentials, the target force to the force-matching should be force from CG vdW potentials = total force from reference atomistic simulations - force from electrostatics with CG topology One thing to note here is that the electrostatic forces with CG topology will not be same as the electrostatic forces in atomistic trajectories. Therefore, to compute electrostic forces in the CG system, you should perform -rerun with CG trajectory and force field itp file for CG system with vdW parameters set to zero. Moreover, you are coarse-graining water molecules into a neutral CG bead, so it won't be able to capture dielectric/polarization effects of water on the electrostatic interactions among charged beads. So you will need to explicitly specify some dielectric constant (such as 78.5) while determining electrostatic interactions in CG system. I hope with this approach you should be able to find meaningful values for CG potentials. Best, Sikandar On Thu, Mar 23, 2017 at 5:28 AM, Rom <[email protected]> wrote: > 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. > -- 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.
