How define a topology in XML file correctly, which contains more than one molecule?

Dongze Wang

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Jan 8, 2020, 7:27:15 AM1/8/20

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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:

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!

Christoph Junghans

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Jan 8, 2020, 8:15:29 AM1/8/20

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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

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Dongze Wang

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Jan 8, 2020, 9:28:35 AM1/8/20

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Thanks, Christoph,

After running "csg_dump" command, there Shows like:

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：

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Christoph Junghans

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Jan 8, 2020, 10:53:38 AM1/8/20

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Ok I understand your issue now, the problem is that you need one mapping file per molecule type, i.e.:

$ cat map.xml

and

$ cat map2.xml
<cg_molecule>

and the use both mapping files after the --cg option, e.g. csg_dump --top topology.xml --cg "map.xml;map2.xml"

Christoph

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