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!
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