2014-11-13 6:38 GMT-07:00 Daniel Allen <[email protected]>: > Hi there, > > I am using csg_dump to read the atoms from a pdb file (as my topology base) > however the program thinks that the mass of each bead (atom) is 1 even > though I specify the weights in the --cg file. > > My beads are defined like so: > > <topology> > <cg_beads> > <cg_bead> > <name>PEO1</name> > <type>PEO</type> > <mapping>PEO</mapping> > <beads> > 1::O1 1::C1 1::H1 1::H2 1::C2 1::H3 1::H4 > </beads> > </cg_bead> > > <cg_bead> > <name>PEO2</name> > <type>PEO</type> > <mapping>PEO</mapping> > <beads> > 2::O1 2::C1 2::H1 2::H2 2::C2 2::H3 2::H4 > </beads> > </cg_bead> > > <cg_bead> > <name>PEO3</name> > <type>PEO</type> > <mapping>PEO</mapping> > <beads> > 3::O1 3::C1 3::H1 3::H2 3::C2 3::H3 3::H4 > </beads> > </cg_bead> > > etc..................... > > > Then once Ive finished defining connectivity I state the maps for the two CG > bead types present in the system: > > <maps> > <map> > <name>PEO</name> > <weights> 16 12 1 1 12 1 1 </weights> > </map> > <map> > <name>PBO</name> > <weights> 16 12 1 1 12 1 1 12 1 1 12 1 1 </weights> > </map> > </maps> > > Any ideas what is going wrong here? I think there is a bit of confusion here: 1.) a pdb file contains no explicit mass information, hence the masses are set to 0. 2.) the mapping file (--cg option) contains no mass information either, the number listed in the "weights" block are the c_is of eqn. 2.5 (http://downloads.votca.googlecode.com/hg/votca-csg-manual-1.2.4.pdf), which aren't real masses. If you choose them equal to the mass, you will get a center of mass mapping though. 3.) The masses of the coarse-grained beads are determined from the masses of the atomic particles (see 2.10 of http://downloads.votca.googlecode.com/hg/votca-csg-manual-1.2.4.pdf) 4.) As all thermodynamic quantities are independent of the masses (Technical point 1.1 of http://www2.mpip-mainz.mpg.de/~bereau/public/thesis.pdf explains that very well), it doesn't really matter they are set in VOTCA as long as you don't need mapped velocities or want to do force matching. 5.) If you want to set the masses in the xml topology you can add a block like <beadtypes> <mass name="C*" value="16"/> </beadtypes> inside <topology>, where C* is the name of the beadtype, matching all C beads (C1,C2,..).
Christoph > > Thanks in advance, > > Dan. > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
