Thanks, Christoph, After running "csg_dump" command, there Shows like: <bead mass="12.01115" name="1" q="-0.106" type="1"/> <bead mass="1.00797" name="2" q="0.053" type="2"/> <bead mass="1.00797" name="3" q="0.053" type="2"/> <bead mass="12.01115" name="4" q="-0.053" type="1"/> <bead mass="1.00797" name="5" q="0.053" type="2"/> <bead mass="12.01115" name="6" q="-0.106" type="1"/> <bead mass="1.00797" name="7" q="0.053" type="2"/> <bead mass="1.00797" name="8" q="0.053" type="2"/> <bead mass="12.01115" name="9" q="-0.159" type="1"/> <bead mass="1.00797" name="10" q="0.053" type="2"/> <bead mass="1.00797" name="11" q="0.053" type="2"/> <bead mass="1.00797" name="12" q="0.053" type="2"/> <bead mass="12.01115" name="13" q="-0.159" type="1"/> <bead mass="1.00797" name="14" q="0.053" type="2"/> <bead mass="1.00797" name="15" q="0.053" type="2"/> <bead mass="1.00797" name="16" q="0.053" type="2"/> <bead mass="12.01115" name="17" q="-0.106" type="1"/> <bead mass="1.00797" name="18" q="0.053" type="2"/> <bead mass="1.00797" name="19" q="0.053" type="2"/> <bead mass="12.01115" name="20" q="-0.053" type="1"/> <bead mass="1.00797" name="21" q="0.053" type="2"/> <bead mass="12.01115" name="22" q="-0.106" type="1"/> <bead mass="1.00797" name="23" q="0.053" type="2"/> <bead mass="1.00797" name="24" q="0.053" type="2"/> I have 24 beads in 2 molecules Boundary Condition: open List of residues: 0 name: m1 id: 0 1 name: m1 id: 0 2 name: m1 id: 0 3 name: m1 id: 0 4 name: m1 id: 0 5 name: m1 id: 0 6 name: m1 id: 0 7 name: m1 id: 0 8 name: m1 id: 0 9 name: m1 id: 0 10 name: m1 id: 0 11 name: m1 id: 0 12 name: m2 id: 12 13 name: m2 id: 12 14 name: m2 id: 12 15 name: m2 id: 12 16 name: m2 id: 12 17 name: m2 id: 12 18 name: m2 id: 12 19 name: m2 id: 12 20 name: m2 id: 12 21 name: m2 id: 12 22 name: m2 id: 12 23 name: m2 id: 12 List of molecules: molecule: 1 m1 beads: 12 0 Name 1:m1:1 Type 1 Mass 12.0112 Resnr 0 Resname m1 Charge -0.106 1 Name 1:m1:2 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 2 Name 1:m1:3 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 3 Name 1:m1:4 Type 1 Mass 12.0112 Resnr 0 Resname m1 Charge -0.053 4 Name 1:m1:5 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 5 Name 1:m1:6 Type 1 Mass 12.0112 Resnr 0 Resname m1 Charge -0.106 6 Name 1:m1:7 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 7 Name 1:m1:8 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 8 Name 1:m1:9 Type 1 Mass 12.0112 Resnr 0 Resname m1 Charge -0.159 9 Name 1:m1:10 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 10 Name 1:m1:11 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 11 Name 1:m1:12 Type 2 Mass 1.00797 Resnr 0 Resname m1 Charge 0.053 molecule: 2 m2 beads: 12 12 Name 1:m2:13 Type 1 Mass 12.0112 Resnr 12 Resname m2 Charge -0.159 13 Name 1:m2:14 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 14 Name 1:m2:15 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 15 Name 1:m2:16 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 16 Name 1:m2:17 Type 1 Mass 12.0112 Resnr 12 Resname m2 Charge -0.106 17 Name 1:m2:18 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 18 Name 1:m2:19 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 19 Name 1:m2:20 Type 1 Mass 12.0112 Resnr 12 Resname m2 Charge -0.053 20 Name 1:m2:21 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 21 Name 1:m2:22 Type 1 Mass 12.0112 Resnr 12 Resname m2 Charge -0.106 22 Name 1:m2:23 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053 23 Name 1:m2:24 Type 2 Mass 1.00797 Resnr 12 Resname m2 Charge 0.053
For that, I have 2 questions, 1. in Manual page 13, <beads>1:ppn:C1...….</beads> What means this "1"? For first molecule? 2. What means "List of residues:"? Thanks again for your time Dongze Wang 在 2020年1月8日星期三 UTC+1下午2:15:29，Christoph Junghans写道： > > > > On Wed, Jan 8, 2020 at 05:27 Dongze Wang <[email protected] > <javascript:>> wrote: > >> Hello, dear all, >> In VOTCA Manual I found an examle of the trajectory which is readed from >> H5MD file. For the trajectory from lammps file should such file look same >> or have some different? I use a small model ( Polyethylene, 2 molecules >> include 24 atoms) and write the XML file as below: >> <topology> >> <molecules> >> <molecule name="m1" nmols="1" nbeads="12" > >> <bead name="1" type="1" mass="12.01115" q="-0.106" /> >> <bead name="2" type="2" mass="1.00797" q="0.053" /> >> <bead name="3" type="2" mass="1.00797" q="0.053" /> >> <bead name="4" type="1" mass="12.01115" q="-0.053" /> >> <bead name="5" type="2" mass="1.00797" q="0.053" /> >> <bead name="6" type="1" mass="12.01115" q="-0.106" /> >> <bead name="7" type="2" mass="1.00797" q="0.053" /> >> <bead name="8" type="2" mass="1.00797" q="0.053" /> >> <bead name="9" type="1" mass="12.01115" q="-0.159" /> >> <bead name="10" type="2" mass="1.00797" q="0.053" /> >> <bead name="11" type="2" mass="1.00797" q="0.053" /> >> <bead name="12" type="2" mass="1.00797" q="0.053" /> >> </molecule> >> <molecule name="m2" nmols="1" nbeads="12" > >> <bead name="13" type="1" mass="12.01115" q="-0.159" /> >> <bead name="14" type="2" mass="1.00797" q="0.053" /> >> <bead name="15" type="2" mass="1.00797" q="0.053" /> >> <bead name="16" type="2" mass="1.00797" q="0.053" /> >> <bead name="17" type="1" mass="12.01115" q="-0.106" /> >> <bead name="18" type="2" mass="1.00797" q="0.053" /> >> <bead name="19" type="2" mass="1.00797" q="0.053" /> >> <bead name="20" type="1" mass="12.01115" q="-0.053" /> >> <bead name="21" type="2" mass="1.00797" q="0.053" /> >> <bead name="22" type="1" mass="12.01115" q="-0.106" /> >> <bead name="23" type="2" mass="1.00797" q="0.053" /> >> <bead name="24" type="2" mass="1.00797" q="0.053" /> >> </molecule> >> <bonded> >> <bond> >> <name>bt1</name> >> <beads> >> m1:1 m1:4 >> m1:4 m1:6 >> m1:6 m1:9 >> m2:13 m2:17 >> m2:17 m2:20 >> m2:20 m2:22 >> </beads> >> </bond> >> <bond> >> <name>bt2</name> >> <beads> >> m1:1 m1:2 >> m1:1 m1:3 >> m1:4 m1:5 >> m1:6 m1:7 >> m1:6 m1:8 >> m1:9 m1:10 >> m1:9 m1:11 >> m1:9 m1:12 >> m2:13 m2:14 >> m2:13 m2:15 >> m2:13 m2:16 >> m2:17 m2:18 >> m2:17 m2:19 >> m2:20 m2:21 >> m2:22 m2:23 >> m2:22 m2:24 >> </beads> >> </bond> >> </bonded> >> </molecules> >> </topology> >> To check it I use "csg_map" command, and then I got: >> I have 24 beads in 2 molecules >> -------------------------------------- >> WARNING: unknown molecule "m1" with id 0 in topology >> molecule will not be mapped to CG representation >> Check weather a mapping file for all molecule exists, was specified in >> --cg separated by ; and the ident tag in xml-file matches the molecule name >> -------------------------------------- >> cannot find: <1:m2:13> in m2 >> an error occurred: >> mapping error: molecule 1:m2:13 does not exist >> >> My mapping file as below >> <cg_molecule> >> <name>m1</name> >> <ident>m1</ident> >> <topology> >> <cg_beads> >> <cg_bead> >> <name>1</name> >> <type>1</type> >> <mapping>A</mapping> >> <beads> 1:m1:1 1:m1:2 1:m1:3 1:m1:4 1:m1:5 1:m1:6 1:m1:7 >> 1:m1:8 </beads> >> </cg_bead> >> <cg_bead> >> <name>2</name> >> <type>2</type> >> <mapping>B</mapping> >> <beads> 1:m1:9 1:m1:10 1:m1:11 1:m1:12 </beads> >> </cg_bead> >> </cg_beads> >> <cg_bonded> >> <bond> >> <name>BondType1</name> >> <beads> >> 1 2 >> </beads> >> </bond> >> </cg_bonded> >> </topology> >> <name>m2</name> >> <ident>m2</ident> >> <topology> >> <cg_beads> >> <cg_bead> >> <name>3</name> >> <type>2</type> >> <mapping>B</mapping> >> <beads> 1:m2:13 1:m2:14 1:m2:15 1:m2:16 </beads> >> </cg_bead> >> <cg_bead> >> <name>4</name> >> <type>1</type> >> <mapping>A</mapping> >> <beads> 1:m2:17 1:m2:18 1:m2:19 1:m2:20 1:m2:21 1:m2:22 >> 1:m2:23 1:m2:24 </beads> >> </cg_bead> >> </cg_beads> >> <cg_bonded> >> <bond> >> <name>BondType1</name> >> <beads> >> 3 4 >> </beads> >> </bond> >> </cg_bonded> >> </topology> >> <maps> >> <map> >> <name>A</name> >> <weights> 12.01115 1.00797 1.00797 12.01115 1.00797 12.01115 >> 1.00797 1.00797 </weights> >> </map> >> <map> >> <name>B</name> >> <weights> 12.01115 1.00797 1.00797 1.00797 </weights> >> </map> >> </maps> >> </cg_molecule> >> >> Is my topology XML file correct? Why this error Shows up? If not, could >> someone give me an example, then I know how such file suppose to be. Thanks! >> > It look like one of the atom is missing or named differently internally, > so you can run “csg_dump —top your_topology.xml” to see the naming. > > Christoph > >> >> -- >> 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] <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/ecc1c17b-d231-4c96-9cc4-3b93b1af864c%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/ecc1c17b-d231-4c96-9cc4-3b93b1af864c%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- > 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/eb995c66-1b1f-4660-8086-13164a5ccc5f%40googlegroups.com.
