2016-08-04 8:57 GMT-06:00 Vikram R <[email protected]>: > Hi Christoph, thanks for your response. > > I could not figure out what the problem was. I solved the problem rather > obliquely, I named each atom to be a part of different residue for the third > molecule and in my mapping file I defined each of the mapping beads > explicitly (=the total number of atoms). This works. Oh well, that is actually the problem ;-)
If you have a molecule with 294 beads like your "G" molecule, your mapping file will need to map the 294 beads. Otherwise only the beads explicitly named in the mapping file will be mapped, i.e. in your case only the first atom. In addition, if multiple beads have the same identifier (i.e. "1:X:ZC" in your case), only the first (or last) bead matching the identifier will be mapped. Your solution was exactly the right thing to do! Christoph > > Thanks a lot again. > > Cheers, > Vikram > > > On Wednesday, August 3, 2016 at 6:47:46 PM UTC+2, Vikram R wrote: >> >> 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. >> >> 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.
