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.
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.
