On Wed, Jan 8, 2020 at 7:28 AM Dongze Wang <[email protected]>
wrote:
> 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:"?
>
Ok I understand your issue now, the problem is that you need one mapping
file per molecule type, i.e.:
$ cat map.xml
<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>
<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>
and
$ cat map2.xml
<cg_molecule>
<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>
and the use both mapping files after the --cg option, e.g. csg_dump --top
topology.xml --cg "map.xml;map2.xml"
Christoph
> 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]> 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
>>
>>>
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>>> .
>>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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--
Christoph Junghans
Web: http://www.compphys.de
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