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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