Using LAMMPS with VOTCA

Satyen Dhamankar

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Feb 21, 2022, 11:59:33 AM2/21/22

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Hello,

I believe this question has been asked quite a few times, but I am still rather in the dark regarding this. How does one go from a LAMMPS dump file to a coarse-grained trajectory?

Much like the tutorials, I am running my own SPCE water simulation. This is the form of my LAMMPS dump file:

ITEM: TIMESTEP
111000
ITEM: NUMBER OF ATOMS
2187
ITEM: BOX BOUNDS pp pp pp
-1.3011386691164584e-01 2.8130113866912254e+01
-1.3011386691164584e-01 2.8130113866912254e+01
-1.3011386691164584e-01 2.8130113866912254e+01
ITEM: ATOMS id type mol xu yu zu
1 1 1 15.9191 21.2231 7.26312
2 2 1 15.1846 20.9848 7.89853
3 2 1 15.9358 20.5644 6.51092
4 1 2 9.47096 4.06014 23.0485
5 2 2 9.95291 3.43993 23.6674
6 2 2 9.25497 4.90974 23.5296
7 1 3 -3.19525 17.8848 16.2274
8 2 3 -3.73498 18.5917 15.7703
9 2 3 -2.992 18.1735 17.163

...

Now, just looking at this trajectory, my molecule of water has no name in particular. So, I am not sure what to put in the <ident> tag in the water.xml file. In the spce tutorial, the csg_map command uses topol.tpr for topology. But it does not seem like sys.data files which define a lammps topology is accepted.

This is my sys.data file:

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

The pdb file I use to generate the water is:

COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.90
HETATM 1 O HOH 1 0.154 1.797 0.015 1.00 0.00 OSPCe
HETATM 2 H HOH 0 1.122 1.767 -0.020 1.00 0.00 HSPCe
HETATM 3 H HOH 0 -0.125 1.206 -0.700 1.00 0.00 HSPCe
CONECT 1 2 3
CONECT 2 1
CONECT 3 1
MASTER 0 0 0 0 0 0 0 0 3 0 3 0
END

How should one proceed with LAMMPS? Is there a specific way one should set up topology in the event I have to run a CG simulation?

I would appreciate any advice you have for me.

Christoph Junghans

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Feb 21, 2022, 12:44:53 PM2/21/22

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I guess the first question is more for the lammps mailing list/
MatSci.org forum in the lammps section. They will know better how to
run an SPCE simulation in LAMMPS. We provide input files for gromacs
in the atomistic/ folder. If you are using the docker container you
should have gromacs installed already.

For the second question, to run a cg simulation you will need to
create a cg initial condition, input settings file (settings.xml),
target rdf and lammps script (in file)

To generate the initial condition you can map an atomic file on a cg
one using csg_map with a mapping file. (csg_map --top atomic.data --cg
mapping.xml --trj atomic.data --out cg.dump)

The mapping file is something you need to write by hand or you can use
the stock tool (http://stock.cmm.ki.si/smt/). You can run csg_dump
--top atomic.data to see what votca reads as molecule name and bead
types to use in the mapping file.

The target rdf you can calculate with csg_stat --top atomic.data --cg
mapping.xml --trj atomic_traj.dump --options settings.xml

The csg manual (https://www.votca.org/csg/index.html) has a section
about input files as well.

Hope that helps,

Christoph

>
> I would appreciate any advice you have for me.
>

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Christoph Junghans
Web: http://www.compphys.de

Satyen Dhamankar

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Feb 21, 2022, 4:54:43 PM2/21/22

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Oh sorry for the misunderstanding. I have already run a SPCE simulation in LAMMPS. I wanted to get the coarse-grained initial config using csg_map, however, i am not sure how to go about making the mapping.xml file using the current directions that you have.

This is what I see when I run csg_dump --top sys.data, this is what I see:

```

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
3 name: DUM id: 3
4 name: DUM id: 4
5 name: DUM id: 5
6 name: DUM id: 6
7 name: DUM id: 7
8 name: DUM id: 8
9 name: DUM id: 9

...

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
5 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41
molecule: 3 H2O1 beads: 3

...

```

Reading the above, molecule name is H2O1. What I dont get, is that the H2 molecules are exactly the same, except for the sr no. If i have a larger molecule without symmetric hydrogens, I imagine the program will not be able to distinguish. How should I go about making the xml file?

This is what I have right now,

<cg_molecule>
<name>CG_WATER</name>
<ident>H2O1</ident>
<topology>
<cg_beads>
<cg_bead>
<name>b1</name>
<type>b</type>
<symmetry>1</symmetry>
<mapping>M1</mapping>
<beads> 1:H2O1:H2 1:H2O1:O1 1:H2O1:H2 </beads>
</cg_bead>
</cg_beads>
</topology>
<maps>
<map>
<name>M1</name>
<weights> 1 16 1</weights>
</map>
</maps>
</cg_molecule>

When I run csg_map --top sys.data

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
cannot find: <1:H2O1:H2> in H2O1
an error occurred:
mapping error: molecule 1:H2O1:H2 does not exist

Where is the error taking place here?

Satyen Dhamankar

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Feb 21, 2022, 5:08:30 PM2/21/22

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Furthermore, where is the resname DUM coming from?

Christoph Junghans

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Feb 21, 2022, 5:50:12 PM2/21/22

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On Mon, Feb 21, 2022 at 3:08 PM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> Furthermore, where is the resname DUM coming from?

It is the residue name and as data file have no residue name, VOTCA
sets it to DUM for dummy.

I think for more complicated molecule, you will need to create xml
topology file.
See towards the end of
https://www.votca.org/csg/input_files.html#advanced-topology-handling.

You can basically do something like:
$ cat topol.xml
<topology>
<molecules>
<box xx="2.8" yy="2.8" zz="2.8" />
<molecule name="H20" nmols="729" nbeads="3">

<bead name="O1" type="O" mass="15.9994" q="-0.82" />
<bead name="H1" type="H" mass="1.008" q="0.41" />
<bead name="H2" type="H" mass="1.008" q="0.41" />
</molecule>
</topology>
then you can use H20:O1 etc in the mapping file. (Check with csg_dump
--top topol.xml first.)

inferring all topology information from all different MD inputs is
sometimes incomplete, hence we have the xml topology format.
Patches for the lammps data reader are always welcome.

Can you try "0:H2O1:H2" instead?

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/34d4cee2-9505-46ea-9ea1-5c07f16c1cffn%40googlegroups.com.

JIANXIN HE

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Apr 3, 2024, 7:28:16 PMApr 3

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Dear Christoph,

Thank you for your clear explanation!!! I have successfully utilized VOTCA for mapping LAMMPS (all atom) following your guidance, specifically using the command:
csg_map --top topol.xml --trj lammps.data --cg mapping.xml --out lmp_cg.dump
I have a small question regarding the output from --out lmp_cg.dump. Is it possible to export this data back into a LAMMPS data file format? If so, how can I specify the styles for the data file? I did not find detailed instructions in the manual.
While using csg_dump --top lammps.data > log, I noticed a kind warning indicating that the VOTCA LAMMPS data reader supports certain styles (angle, atom, bond, full, molecule).
Or it only --out the dump file? Thank you for your assistance.

Best,
J.

Christoph Junghans

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Apr 4, 2024, 9:53:28 AMApr 4

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On Wed, Apr 3, 2024 at 5:28 PM 'JIANXIN HE' via votca
<vo...@googlegroups.com> wrote:
>
> Dear Christoph,
>
> Thank you for your clear explanation!!! I have successfully utilized VOTCA for mapping LAMMPS (all atom) following your guidance, specifically using the command:
> csg_map --top topol.xml --trj lammps.data --cg mapping.xml --out lmp_cg.dump
> I have a small question regarding the output from --out lmp_cg.dump. Is it possible to export this data back into a LAMMPS data file format? If so, how can I specify the styles for the data file? I did not find detailed instructions in the manual.

No, that is not implemented.

> While using csg_dump --top lammps.data > log, I noticed a kind warning indicating that the VOTCA LAMMPS data reader supports certain styles (angle, atom, bond, full, molecule).
> Or it only --out the dump file? Thank you for your assistance.

That is correct, the lammps reader can only digest certain styles in
the input file.

For both issues, patches are welcome, after all VOTCA is open-source.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/95c7f44c-b6b5-4dd9-af72-826b2b1415f9n%40googlegroups.com.

jianxin he

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Apr 5, 2024, 3:40:03 PMApr 5

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Got it! Thank you so much!

Best,
J

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