Dear Victor,
first of all appreciate your help. I followed the steps you told me.
My atomistic system consists on 20 polyethylene molecules with 50
repeating units per molecule, and i want to map 5 PE monomers per bead
in order to produce chains with 10 beads. Since lammps dump files
doesn't give the information of atom names necessary to identify each
atom on the .xml mapping file, i decided to use a .pdb file. In this
case, my topol.xml file looks like this:
<topology base="PE_50CRU_20.pdb">
<molecules>
<clear/>
<define name="PE" first="1" nbeads="302" nmols="20"/>
</molecules>
</topology>
Then, using topol.xml, lammps dump file, and .xml mapping file, i
managed to generate my coarse-grained trajectory file, doing:
csg_map --top topol.xml --trj PE.dump --cg cg_polyethylene.xml --out
cg.gro
In order to create my coarse-grained topology file i did:
csg_gmxtopol --top topol.xml --cg_polyethylene.xml --out topol.top
Until now everything seems to work fine, although when i check cg.gro
file using VMD ijust get unconnected dots instead of chains with 10
beads. Is it normal?
The <cg_bonded> section of my mapping file looks like:
<cg_bonded>
<bond>
<name>bond</name>
<beads>
A1 B1
B1 B2
B2 B3
B3 B4
B4 B5
B5 B6
B6 B7
B7 B8
B8 A2
</beads>
</bond>
<angle>
<name>angle</name>
<beads>
A1 B2 B3
B2 B3 B4
B3 B4 B5
B4 B5 B6
B5 B6 B7
B6 B7 B8
B7 B8 A2
</beads>
</angle>
</cg_bonded>
Type-A and type-B beads stand for terminal and non-terminal chain
beads.
The coarse-grained trajectory file generated by csg_map looks like:
what a nice title
200
1PE A1 1 11.118 11.032 6.797
1PE B1 2 10.887 11.697 5.624
1PE B2 3 16.129 10.913 5.547
1PE B3 4 15.321 10.929 5.524
1PE B4 5 24.939 17.177 4.864
1PE B5 6 16.785 8.389 6.152
1PE B6 7 18.330 10.342 5.144
1PE B7 8 18.497 8.256 5.028
1PE B8 9 17.382 12.321 6.009
1PE A2 10 18.825 11.597 4.970
2PE A1 11 24.037 17.481 5.708
2PE B1 12 23.682 19.766 5.909
2PE B2 13 25.950 18.976 5.891
2PE B3 14 26.427 22.298 5.572
2PE B4 15 23.541 17.518 6.789
2PE B5 16 30.227 17.888 6.137
2PE B6 17 32.363 17.257 4.913
2PE B7 18 36.061 19.905 5.503
2PE B8 19 37.420 19.406 5.820
2PE A2 20 34.601 19.822 5.938
........
........
20PE A1 191 31.065 26.259 39.018
20PE B1 192 32.454 27.239 38.932
20PE B2 193 35.126 29.266 38.107
20PE B3 194 28.876 27.833 38.815
20PE B4 195 35.476 28.096 39.252
20PE B5 196 34.333 29.888 39.837
20PE B6 197 21.535 23.948 38.469
20PE B7 198 18.205 35.272 38.868
20PE B8 199 16.173 31.577 39.521
20PE A2 200 8.468 35.507 38.068
0.00000 0.00000 0.00000
And the coarse-grained topology file generated by csg_gmxtopol, looks
like:
[ moleculetype ]
PE 3
[atoms]
; nr type resnr residue atom cgnr charge mass
1 A 1 RES A1 1 0.000000 0.000000
2 B 1 RES B1 2 0.000000 0.000000
3 B 1 RES B2 3 0.000000 0.000000
4 B 1 RES B3 4 0.000000 0.000000
5 B 1 RES B4 5 0.000000 0.000000
6 B 1 RES B5 6 0.000000 0.000000
7 B 1 RES B6 7 0.000000 0.000000
8 B 1 RES B7 8 0.000000 0.000000
9 B 1 RES B8 9 0.000000 0.000000
10 A 1 RES A2 10 0.000000 0.000000
[ bonds ]
1 2 1 ; 1:bond:1
2 3 1 ; 1:bond:2
3 4 1 ; 1:bond:3
4 5 1 ; 1:bond:4
5 6 1 ; 1:bond:5
6 7 1 ; 1:bond:6
7 8 1 ; 1:bond:7
8 9 1 ; 1:bond:8
9 10 1 ; 1:bond:9
[ angles ]
1 3 4 1 ; 1:angle:1
3 4 5 1 ; 1:angle:2
4 5 6 1 ; 1:angle:3
5 6 7 1 ; 1:angle:4
6 7 8 1 ; 1:angle:5
7 8 9 1 ; 1:angle:6
8 9 10 1 ; 1:angle:7
After taking a look on the files generated i cannot see any problem,
but i wonder why i cannot see chains on VMD.
Concerning the package to run the iterative proceedure i'm pretending
to use gromacs.
Thanks so much for your help.
All the best,
Sacha
On Jun 21, 11:26 am, Victor Ruehle <[email protected]> wrote:
> Dear Sacha,
>
> it would be good to know a bit more about your system to evaluate
> which is the simplest way (how complex is your molecule on
> coarse-grained level?). You will be able to parse your lammps
> trajectories and use them as a topolgoy, but using lammps for the
> iterative process would require some modifications of the scripts.
>
> VOTCA supports reading of lammps trajectories, if you name them with
> the ending .dump. These can also be used as topologies by specifying
> an additional xml file. I tested it using the following in the lammps
> script:
>
> dump id all custom 100 system.dump x y z fx fy fz (forces are optional)
>
> This can be used directly as trajectory, but for a topology and
> additional file specifying the molecule information is necessary. If
> you want to use that as a topology, you'lll have to specify an
> additional xml file topol.xml where molecules and names are specified
> (in the manual is a similar example using a pdb file).
> <topology base="system.dump">
> <molecules>
> <clear/>
> <define name="water" first="1" nbeads="3" nmols="1000"/>
> </molecules>
> </topology>
>
> then you can use e.g:
> csg_map --top topol.xml --trj system.dump --cg bla.xml ...
>
> To summarize: the missing bit is this xml file, you can use .pdb,
> .dump, .tpr as base files. Lammps can probably directly write molecule
> information. I didn't had it in my example and am not so familiar with
> lammps, so it's not implemented yet. Be aware that csg_gmxtopol will
> require some manual adjustments of the topology file.
>
> If you want to use IBI or IMC: the scripts to run lammps simulations
> are not yet implemented since we didn't use it here. One way is to run
> the iterative procedure using gromacs (which should not be hard to
> setup and i can guide you to a proper example depending on your
> coarsee-grained topology). Otherwise, if you want to use lammps for
> coarse-grained iterations (it needs to support tabulated potentials
> then), you'll have to modify a few scripts (~ 3 scripts and maybe 30
> lines of code).
>
> Let me know which way you would prefer and we can post further details
> how to proceed.
>
> Cheers,
> Victor
>
> 2011/6/21 Sacha Mould <[email protected]>:
>
> > Hi all,
>
> > i wonder if someone already runned votca from Lammps atomistic dump
> > files.Lammps is capable to dump .xtc trajectory file, but i'm having
> > problems to get the .tpr file in order to obtain coarsed-grained .top
> > and .gro files using csg_map and csg_gmxtopol commands. I'm interested
> > to run IBI and IMC simulations and i'm using Votca 1.1.2 release.
>
> > I appreciate if someone can give me a tip.
>
> > Many regards,
>
> > Sacha
>
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>
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