Dear Sikandar, The answers two your questions can be found in the original paper of Will Noid: http://m.jcp.aip.org/resource/1/jcpsa6/v128/i24/p244114_s1 If you read this paper carefully, you will see that coordinates and forces can have different mapping schemes and indeed it is possible to neglect the forces on H-atoms.
Our experience that FM works the best (again, from the point of view of reproducing a pair potential) when the center of mass of a molecule is used. This also helps to avoid redefinition of the mass of the coarse-grained bead in order to preserve correct sampling in the momentum space. Best, Denis On Oct 7, 9:46 pm, Sikandar Mashayak <[email protected]> wrote: > Hi > > Force Matching algorithm tries to match forces on CG sites. Forces on CG > site are determined by using all-atom MD trajectory and Mapping scheme > utilized to map atoms to CG site. This way, if OW is chosen to be CG for > SPC/E water then only the Force acting on OW will be reproduced. > > My question is, what happens to the information about forces on HW atoms? > The trajectory of OW atoms in all-atom MD also depend on forces on HW atoms. > Is it not erroneous to neglect these forces in FM alorithm? > > 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.
