2016-08-03 10:47 GMT-06:00 Vikram R <[email protected]>: > Dear Votca users, I am using the latest version of VOTCA. > I am facing an issue with csg_map while trying to map an all-atom trajectory > that contains 3 kinds of molecules to a CG trajectory. Two of the molecules > I am coarse-graining are working fine, the other which I am not > coarse-graining (I want it to stay at the all-atom resolution after CG > mapping) doesn't seem to work. > > I map the third molecule to 1 all-atom to 1 CG bead but in the final > trajectory I just get one bead with all the atoms combined. > > My expected result is to have as many number of beads as the atoms for the > third molecule. > > Here is the command I use, > ~/votca_latest/bin/csg_map --top top.xml --trj mv.dump --cg > "water.xml;hexane.xml;graphene.xml" --out CG.gro > > > My top.xml reads, > <topology base= "comp1.pdb"> > <molecules> > <clear/> > <define name="WAT" first="1" nbeads="3" nmols="5450"/> > <define name="HEX" first="16351" nbeads="6" nmols="1200"/> > <define name="G" first="23551" nbeads="294" nmols="1"/> > </molecules> > </topology> > > The issue seems to be with my third molecule (graphene.xml) as the csg_dump > gives me what I want, > > My third molecule mapping looks like this, > > <cg_molecule> > <name>CG_G</name> > <ident>G</ident> > <topology> > <cg_beads> > <cg_bead> > <name>G</name> > <type>G</type> > <mapping>G</mapping> > <beads>1:X:ZC</beads> > </cg_bead> > </cg_beads> > </topology> > <maps> > <map> > <name>G</name> > <weights>1</weights> > </map> > </maps> > </cg_molecule> > > Please let me know if you figure out where the problem might be. I'd really > appreciate any help. My guess is that "1:X:ZC" isn't the right identifier for the atom.
Have a look at the output of $ csg_dump --top top.xml --cg "water.xml;hexane.xml;graphene.xml" or $ csg_dump --top top.xml --cg graphene.xml --map-ignore "HEX;WAT" (for shorter output) Cheers, Christoph > > Thanks a lot in advance. > > Cheers, > Vikram Reddy Ardham, > PhD student, > Theoretical Physical Chemistry group, > TU Darmstadt, Germany > > -- > 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. -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
