yeah, sounds interesting .. so i will do two test cases, in first - taking full trajectory from gromacs, I will do mdrun -rerun and exclude any CG1-CG1 interactions then use the output trajectory to FMatch CG1-CG2, CG2-CG2 simultaneously.
In second, will remove CG1-CG2 interactions as well to get CG2-CG2 and vice-versa. Will get back to you once i get the results. Also, on another thought, I understand this varies from case to case, but how many frames are usually ok for Fmatch to converge and what value of tolerance that is limit on error (3rd colmn of cg-cg.force) is recommended to decide convergence... thanks sikandar On Fri, Mar 11, 2011 at 4:06 AM, Victor Ruehle <[email protected]> wrote: > FM tries to fit the total force, if you have some fixed components, > you'll have to subtract them first, or exlcude in a rerun. so in your > case you would have to exclude CG1-CG1 interactions or subtract > corresponding forces (csg_fmatch --force-trj, documentation will > follow). So csg_fmatch only does the mapping of total forces in > trajectory + fit of all specified interactions at once. > > So separation is an issue, and you'll have to decide what works best > for you particular system. I don't think there is a general rule how > to proceed. So you can exclude/subtract CG1-CG1, then fit CG1-CG2 + > CG2-CG2 simultaneously or try to exclude one of em as well and do the > fit individually. In any case I'm interested how it works out and can > give advise on how to set this up in VOTCA/gromacs. > > 2011/3/11 Sikandar Mashayak <[email protected]>: > > I am kinda confused here. Lets say I have mixture of two molecules, one > with > > more than one atoms and second one is just simple one atom molecule, call > it > > as CG1. > > Then I wish to coarse-grain multi-atom molecule to its COM site, call it > as > > CG2 and now determine what is the effective CG potentials between > CG2-CG2, > > CG1-CG2, I dont have to worry about CG1-CG1 which I know already. > > The trajectory contains the force information due to all possible > > interactions. So to determine CG2-CG2, do I have to eliminate any > > interaction between CG2-CG1, and same for CG1-CG2 i.e. eliminate > > CG2-CG2,CG1-CG1. Or FM takes of these by itself. That is to say when > > computing CG2-CG2 it only considers force acting on CG2 site only because > of > > CG2-CG2 interaction and not any other. > > Yeah, it would be great if you could forward me the paper you submitted > in > > regard to this topic. > > thanks > > sikandar > > On Thu, Mar 10, 2011 at 5:34 PM, Victor Ruehle <[email protected]> wrote: > >> > >> Hey, > >> > >> how do you want do describe interactions between coarse-grained and > >> atomistic molecules? Each atom with coarse-grained site? How many > >> different atom types and with that interactions will you have then? > >> Also be aware that mixing resolutions might lead to additional > >> problems. > >> > >> Currently the only way to keep one molecule at atomistic resolution in > >> force matching is by specifying a 1:1 mapping files, which maps each > >> atom to one coarse-grained bead. However, what you plan to do is not > >> trivial since your trajectory has the full forces, also the ones which > >> you don't want to parametrize. If you can do a clean splitting, either > >> by excluding interactions, or by subtracting already known ones (this > >> feature was added in 1.1) this might work. We recently submitted a > >> paper on this, I can send you the draft if you want. > >> > >> Victor > >> > >> 2011/3/10 Sikandar Mashayak <[email protected]>: > >> > Hi > >> > I want to perform a Force Matching on a reference system which > contains > >> > two > >> > types of molecules. I am planning to CG one of it and keep the other > in > >> > all-atom description. > >> > So I am wondering how do I specify options in fmatch.xml file? Will I > >> > have > >> > to specify non-bonded interactions for CG-CG and each pair of CG-atoms > >> > of > >> > other molecule? > >> > thanks > >> > sikandar > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "votca" group. > >> > To post to this group, send email to [email protected]. > >> > To unsubscribe from this group, send email to > >> > [email protected]. > >> > For more options, visit this group at > >> > http://groups.google.com/group/votca?hl=en. > >> > > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups > >> "votca" group. > >> To post to this group, send email to [email protected]. > >> To unsubscribe from this group, send email to > >> [email protected]. > >> For more options, visit this group at > >> http://groups.google.com/group/votca?hl=en. > >> > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
