On Wed, Jan 8, 2020 at 05:27 Dongze Wang <[email protected]> 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]. > 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/CAHG27e5s95BvwFJeaT%3DAgXiXLrmSLjs75J4f941GvVdc0LBL%3DQ%40mail.gmail.com.
