Hi there,
I am trying to read in a LAMMPS dump file for a simulation of liquid butane
into csg_stat as a simple example of how to map and process LAMMPS
trajectories, before moving onto my more complex system of long chain
polymers.
I know that there are a couple of previous questions regarding LAMMPS
topologies but I cannot quite get it working.
First I tried using a .pdb file specified in my topol.xml file but this
gave an error:
"an error occurred:
P-P.pdb: unknown topology format" which I find strange because in the
manual it gives an example of using a pdb file for topology, any ideas why
this error would occur?
Anyway, I then decided to try and use the lammps .dump file as the topology
so topol.xml now looks like this:
<topology base="atoms_nvt_prod.dump">/ITEM
<molecules>
<clear/>
<define name="B" first="1" nbeads="14" nmols="100"/>
</molecules>
</topology>
So I have defined one molecule type which consists of 14 atoms and there
are 100 molecules in the system beginning at atom 1.
I think the problem lies in the coarse-grained mapping file. When listing
atoms which belong to a particular bead, if the syntax is
RESID:RESNAME:ATOMNAME then I'm struggling to work out what they should be
for my system.
Here is the top of my dump file:
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
13916
ITEM: BOX BOUNDS pp pp pp
-27.8209 27.7639
-27.7926 27.8726
-27.6615 27.7715
ITEM: ATOMS id type x y z
12765 2 -21.1019 -18.5716 -26.1089
12766 1 -21.1227 -18.563 -24.9982
12768 1 -20.1424 -19.0188 -26.4462
9768 1 -25.3608 -20.7513 -21.6347
9766 2 -25.8077 -20.8022 -20.6188
9762 1 -23.0727 -20.4904 -19.9854
9764 1 -25.494 -18.664 -19.9916
9763 2 -25.1286 -19.6941 -19.7923
9767 1 -26.8648 -20.4951 -20.7686
9769 2 -25.9722 -22.1004 -19.9808
9760 1 -23.565 -19.281 -21.2077
9759 2 -23.6425 -19.548 -20.132
13105 2 -25.5908 -19.0274 -24.4098
638 2 -22.4319 -26.8526 -26.9045
9772 1 -26.1693 -22.9545 -20.6634
13106 1 -25.5393 -19.9713 -24.9935
11466 1 -22.2057 -26.6297 -23.7546
11454 1 -26.0494 -24.6427 -23.5225
11458 1 -24.8424 -26.6034 -24.4689
3362 1 -20.4076 -20.3751 -20.0356
639 1 -22.2076 -27.6125 -26.1257
etc ...
Would RESID just be 1? There is no information about residues in the dump
file, does there need to be? It is possible to printout the molecule number
in the dump file.
For RESNAME, I wouldn't know what to use either.
For ATOMNAME I could use the atom type, so atom name would be "2" for C and
"1" for H?
The choice for these labels would be more obvious from my .pdb file:
HETATM 1 C7 B A 1 -5.985 7.723 -2.9591.00 0.00
C
HETATM 2 H71 B A 1 -5.479 7.242 -2.1481.00 0.00
H
HETATM 3 H72 B A 1 -5.406 7.617 -3.8531.00 0.00
H
HETATM 4 C8 B A 1 -6.944 7.270 -3.1001.00 0.00
C
HETATM 5 C9 B A 1 -7.523 7.376 -2.2061.00 0.00
C
HETATM 6 H81 B A 1 -6.818 6.231 -3.3221.00 0.00
H
HETATM 7 H82 B A 1 -7.450 7.750 -3.9111.00 0.00
H
HETATM 8 H91 B A 1 -7.017 6.896 -1.3951.00 0.00
H
HETATM 9 C10 B A 1 -8.482 6.923 -2.3471.00 0.00
C
HETATM 10 H92 B A 1 -7.648 8.415 -1.9831.00 0.00
H
HETATM 11 H101 B A 1 -8.357 5.884 -2.5691.00 0.00
H
HETATM 12 H102 B A 1 -8.988 7.404 -3.1581.00 0.00
H
HETATM 13 H73 B A 1 -6.112 8.781 -2.7321.00 0.00
H
HETATM 14 H103 B A 1 -9.071 7.031 -1.4361.00 0.00
H
So for the first atom it would be 1:B:C7 for example?
Any help would be greatly appreciated,
Thanks, Dan.
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