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 -- 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.
