LAMMPS is now fully supported for IBI and IMC in VOTCA 1.3-dev! Please have a look at: <https://code.google.com/p/votca/source/browse/?repo=csg-tutorials#hg%2Fspce%2Fibi_lammps>
Cheers, Christoph 2012/8/27 Christoph Junghans <[email protected]>: > 2012/8/27 karthik kumar <[email protected]>: >> Non-bonded potentials in my system are 2 body interactions.\ > That will work with Gromacs as well and basically all tutorials deal > with 2 body interactions. > Have a look at the SPCE example for a single component system and > propane for a two component system. > >> Now, I want to write scripts to make use of VOTCA for my LAMMPS MD package. > Nice. > >> can you please give some ideas from where to start, > Fix you will need to build and install the development version of votca, see: > <http://code.google.com/p/votca/wiki/Installing#From_Source> > and especially: > <http://code.google.com/p/votca/wiki/Installing#Development_Version> > > Then have a look at the following 4 scripts in csg/share/scripts/inverse > initialize_step_generic_gromacs.sh potential_to_gromacs.sh > prepare_generic_gromacs.sh run_gromacs.sh > > you will have to write LAMMPS equivalents of those. > > - potential_to_lammps.sh: tells VOTCA how to convert a tabulated > potential file from VOTCA format into lammps format > + VOTCA format is x Potential(x) flag(x), where flag is i="in range", > o="out range", u="undefined" > - prepare_generic_lammps.sh: generates input data for the 1st > iteration step from user input in the main directory > + usually copies over initial configuration file > - initialize_step_generic_lammps.sh: generates input data at the > beginning of every iteration step from the outcome of the last step > + convert all potential to LAMMPS format > + copy for initial condition > + additional consistency check if needed > - run_lammps.sh: how to actually execute lammps (have a look at > run_espresso.sh as Espresso is more similar to LAMMPS as gromacs) > + generate a LAMMPS scripts > + run it > + wallclock time check if needed. > > VOTCA support the Espresso package as an MD backend, but Espresso is > not as well integrated in the analysis tools as LAMMPS. > > Try to write potential_to_lammps.sh and run_lammps.sh first, I write > the other ones. > > As LAMMPS has no topology format, you will have to write a xml > topology file, see the manual for that. > > Cheers, > > Christoph >> >> thanks >> karteek kumar >> >> >> On Mon, Aug 27, 2012 at 8:42 PM, Christoph Junghans <[email protected]> >> wrote: >>> >>> Hi karteek, >>> >>> you will not get an answer faster if you ask 3 times, this will >>> actually have the opposite effect :-) >>> >>> The support for LAMMPS in VOTCA is very basic, which means all VOTCA >>> analysis tools (csg_*) can read LAMMPS dump files and analyze them. >>> Iterative Boltzmann inversion (IBI) using LAMMPS as an MD backend is >>> not implemented yet, mainly due to a lack of development power/time >>> and lack of interest by the VOTCA users. >>> It is not hard to implement, you will have to write 5 scripts - I can >>> help you with that. >>> >>> On the other hand the only reason to use LAMMPS with VOTCA would be if >>> you want to use feature, which is not implemented in Gromacs. IBI on >>> non-bonded 3-body interactions is the only thing I could think of. >>> For non-bonded 2-body interactions Gromacs is usually sufficient. >>> >>> Cheers, >>> >>> Christoph >>> >>> 2012/8/26 karthik kumar <[email protected]>: >>> > Hi users and developers, >>> > I am very beginner to VOCTA. >>> > >>> > I can using LAMMPS package to run MD. >>> > Now I want to calculate non-bonded parameters with iterative boltzmann >>> > inversion ( or any other method) . >>> > >>> > How can i do that with VOCTA. >>> > >>> > Thanks in advance >>> > >>> > karthik kumar >>> > >>> > -- >>> > You received this message because you are subscribed to the Google >>> > Groups "votca" group. >>> > To view this discussion on the web visit >>> > https://groups.google.com/d/msg/votca/-/sCZKw3EnpKgJ. >>> > To post to this group, send email to [email protected]. >>> > To unsubscribe from this group, send email to >>> > [email protected]. >>> > For more options, visit this group at >>> > http://groups.google.com/group/votca?hl=en. >>> > >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]. >>> For more options, visit this group at >>> http://groups.google.com/group/votca?hl=en. >>> >> > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > > -- > Christoph Junghans > Web: http://www.compphys.de -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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