2017-09-11 2:33 GMT-06:00 <[email protected]>: > Dear Christoph, > > I fix the files and now the mapping works even for larger system with 20 > different molecules. > As you can see each molecule contains beads of various types and masses. > How do I define the mass of each bead type? You can add a block in the xml <topology base="data.mapx.pdb"> <molecules> <clear/> ... </molecules> <beadtypes> <mass name="C1" value="16.0"/> <mass name="C2" value="15.9"/> ... </beadtypes> <</topology>
Also what do you need the masses for? As long as you only calculated static properties (everything based on the position, they won't matter.) Christoph > Should I add this information to the topolgy file (attached)? > > Regards, > Erez > > > בתאריך יום שלישי, 29 באוגוסט 2017 בשעה 20:54:37 UTC+3, מאת Christoph > Junghans: >> >> 2017-08-29 8:02 GMT-06:00 <[email protected]>: >> > Hi Christoph, >> > >> > I followed the manual instructions and fist created input files for >> > mapping >> > single chain. >> > My goal is to map the atomistic chains into 10-beads coarse-grained >> > chains. >> > The atomsitic chains have different structures. >> That is pitty, for molecules of the same type, you can just use one >> mapping file. >> >> > The files are attached. >> > I run cg_map and it works fine: >> > cg_map --top topo_1_molecule.xml --trj trj_1_molecule.pdb --cg >> > cg_1st_molecule.xml --out cg_1molecule.pdb >> > >> > I then tried to add another chain as another molecule, using 2 types of >> > topolgy files (v1 and v2 following the 2 examples in section 3.3 in the >> > manual respectively), and run: >> > cg_map --top topo_2_molecules_v1.xml --trj trj_2_molecule.pdb --cg >> > "cg_1st_molecule.xml:cg_2nd_molecule.xml " --out cg_2molecules.pdb >> > >> > for topology file "topo_2_molecules_v1" i've got this error": >> > cannot find <1:SL2:c1> in SL2 >> You can use >> $ csg_dump --top topo_2_molecules_v1.xml >> to look at how VOTCA sees the topology. >> >> For a quick look at the above output, I saw that the residue name of >> the 2nd molecule wasn't read correctly. (and hence the is no 1:SL2:c1 >> with SL2 being the residue name) >> I guess this because the residue numbering in the pdb is relative to >> the molecule, but it should be absolute (fix pdb attached) >> >> With that change: >> $ csg_map --top topo_2_molecules_v1.xml --trj trj_2_molecule.pdb --cg >> "cg_1st_molecule.xml;cg_2nd_molecule.xml" --out cg_2molecules.pdb >> runs, but fails with "cannot find map c11f14hc6", which basially means >> you need to add the "c11f14hc6" to cg_2nd_molecule.xml >> >> Christoph >> > >> > for topology file "topo_2_molecules_v2" i've got this error": >> > RenameMolecules: num molecules smaller than >> > (I guess this error indicates that i defined only 2 molecules while the >> > trj >> > file contains 20( >> > >> > Any suggetions how to proceed? >> > >> > Thanks a lot, >> > Best regards, >> > Erez >> > >> > >> > >> > >> > בתאריך יום חמישי, 24 באוגוסט 2017 בשעה 20:16:12 UTC+3, מאת Christoph >> > Junghans: >> >> >> >> 2017-08-24 8:40 GMT-06:00 <[email protected]>: >> >> > Hello votca users, >> >> > >> >> > I'm trying to create topology and mapping files for coarse-graining >> >> > polymer >> >> > system with various molecule types (i.e. chains with variuos length >> >> > and >> >> > chemical structure). >> >> > >> >> > I'm using atomistic lammps trajectory or .pdb files as basis. >> >> > >> >> > Would anyone advise what should be the correct form of topology and >> >> > mapping >> >> > files for such system? >> >> Have a look at the manual: doc.votca.org/manual.pdf, section 3.1 for >> >> the mapping and section 3.3 for xml topology file (which will work >> >> best with LAMMPS). >> >> >> >> And I would start with a single repeat unit of the polymer. If the >> >> unit isn't too big you can use the stock tool >> >> http://stock.cmm.ki.si/smt/ interactively. >> >> >> >> Christoph >> >> > >> >> > Regards, >> >> > Erez >> >> > >> >> > -- >> >> > 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. >> >> >> >> -- >> 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. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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