Hello.
I am trying to build a coarse-grained simulation using the VOTCA software. I am running a simple test with SPCE water.
I want to coarse-grain SPCE water into a single bead and run a simple IBI parameterization.
However, I am having trouble setting up the mapping file. In VOTCA, bead definition requires residue id: residue name: atom name. How does one assign a residue/molecule name in the sys.data file?
When I execute csg_dump --top sys.data on my SPCE water, i get the following output:
WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles:
angle
atom
bond
full
molecule
These styles use the following formats in the atom block:
atom-ID molecule-ID atom-type charge x y z
atom-ID molecule-ID atom-type charge x y z nx ny nz
atom-ID molecule-ID atom-type x y z
atom-ID molecule-ID atom-type x y z nx ny nz
atom-ID atom-type x y z
atom-ID atom-type x y z nx ny nz
I have 2187 beads in 729 molecules
Boundary Condition: orthorhombic
Box matix: 2.8 0 0
0 2.8 0
0 0 2.8
List of residues:
0 name: DUM id: 0
1 name: DUM id: 1
2 name: DUM id: 2
.
.
.
List of molecules:
molecule: 1 H2O1 beads: 3
0 Name O1 Type O1 Mass 15.9994 Resnr 0 Resname DUM Charge -0.82
1 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41
2 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41
molecule: 2 H2O1 beads: 3
3 Name O1 Type O1 Mass 15.9994 Resnr 1 Resname DUM Charge -0.82
4 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41
.
.
.
As you can see, in list of molecules, both H atoms have the same name, type, mass, resnr, resname – everything. In the event I have a slightly complicated molecule with H atoms not being symmetric, I will not be able to distinguish between these atoms.
This is how my sys.data file looks like:
#LAMMPS data file generated
2187 atoms
2 atom types
1458 bonds
1 bond types
729 angles
1 angle types
0 dihedrals
0 dihedral types
0.0000000000000000e+00 2.8000000000000000e+01 xlo xhi
0.0000000000000000e+00 2.8000000000000000e+01 ylo yhi
0.0000000000000000e+00 2.8000000000000000e+01 zlo zhi
Masses
1 15.99940 # OSPCe
2 1.00800 # HSPCe
Atoms
1 1 1 -0.82000 26.4795641655 13.9845510766 10.8342774813 0 0 0
2 1 2 0.41000 26.0120845362 13.3829183164 11.4331512727 0 0 0
3 1 2 0.41000 26.3193693668 14.8622934936 11.2114417372 0 0 0
4 2 1 -0.82000 14.0145593114 1.5446899105 26.5086662016 0 0 0
5 2 2 0.41000 14.6271886820 1.6095611553 25.7605846713 0 0 0
6 2 2 0.41000 13.1417198035 1.6740140444 26.1089494746 0 0 0
7 3 1 -0.82000 4.6668218860 23.2721041307 17.0845511689 0 0 0
My question is: how does one provide a name to each atom in a molecule, and provide a molecule name?
I know of the group command, and I do have a
group spce molecule 1 2 in my sys.settings file, not in the sys.data file. I was directed here from thr VOTCA mailing list … '._.
I would appreciate any advice you have for me!