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.
