2013/9/18 Scott Sides <[email protected]>:
> Ok, I'll get on that. Couple of questions first
>
> I'm working from the manual for votca 1.2.3 and some of the commands arent
> working for the propane
> tutorial. For example
>
> csg_gmxtopol --top topol.tpr --cg propane.xml --out out.top
>
>
> Isnt working for me. For one thing... I dont see a topol.tpr file. When I
> try
>
>
> stc-24459s:single_chain ssides$ csg_dump --top topol.top
>
> an error occurred:
>
> input format not supported: topol.top
>
>
> is the result. The topol.top file is the cloest thing to a topology file
> that the manual refers to.
Sorry, I wasn't really clear yesterday about how to get theLAMMPS input files.
csg_gmxtopol will not be really helpful for that as it create a
coarse-grained gromacs (gmx) topology.
Anyhow for LAMMPS you will need:
- data file, easiest is to convert the gro file
$ awk '(NR>2){print $4,$5,$6}' spce.gro
will give you the coordniates to start with.
- lammps script, that is a bit more tricky, easiest will be to start
from spce/ibi_lammps/spce.in and change pair_styles
- topol.xml - see my previous email
- settings.xml - use the on of the gromacs example and add the lammps
options from spce/ibi_lammps
- bonded interactions, you will need to convert table_[ab]1.xvg to the
format of tabulated bonds and angle in lammps.
Hope that helps to get started,
Christoph
>
>
> Thanks,
>
> Scott
>
>
> On Wednesday, September 18, 2013 2:46:14 PM UTC-6, Scott Sides wrote:
>>
>> Christoph,
>>
>> I'd like to run the propane example with lammps (I've managed to get
>> the spce example running and its very informative).
>> I've looked at the lammpsreader.cc page you've listed in other posts. I
>> was wondering if you could give a quick outline of steps
>> needed to bring the propane example up to speed with lammps.
>>
>>
>> thanks,
>> Scott W Sides (NREL)
>>
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Christoph Junghans
Web: http://www.compphys.de
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