Hi Itsuo, sorry for the delay, but sometimes it might take a week until I come around to answer. And again, please send your message to our mailing list (votca@googlegroups.com) so that other can learn from the answers.
Have a look into share/scripts/inverse in the source or share/votca/scripts/inverse in the installation. $ ls *espresso* calc_pressure_espresso.sh calc_rdf_espresso.sh functions_espresso.sh initialize_step_generic_espresso.sh potential_to_espresso.sh prepare_generic_espresso.sh run_espresso.sh of that calc_rdf_espresso.sh functions_espresso.sh initialize_step_generic_espresso.sh potential_to_espresso.sh prepare_generic_espresso.sh run_espresso.sh are the scripts you will have create to support a new simulation backend (replace "espesso" with "namd" when renaming and also add these scripts to csg_table) To calculate the rdf you could either use an external program like vmd: <http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21534.html> and put that command in your calc_rdf_namd.sh and run csg_resample on the output (see end of calc_rdf_espresso.sh) or use csg_stat with xml topology (see section 3.3 of votca manual). Cheers, Christoph 2013/5/15 Itsuo HANASAKI <hanas...@me.es.osaka-u.ac.jp>: > Dear Dr. Christoph Junghans > (CC: VOTCA development team) > > We had received a reply from you some time ago as follows, and I would like > to know > some more specific information on how to use the data of radial distribution > funciton > as the only(?) input of VOTCA. Currently we have not been able to figure out > how to > coarse-grain the system without GROMACS-formatted files because > manuals/tutorials > of VOTCA are written on GROMACS basis. If it is also possible to convert all > the necessary > data obtained by NAMD into GORMACS ones using existing tools, we would > appreciate > the instructions on the information (i.e., URLs) of tools. > > On Tue, 5 Mar 2013 19:33:39 -0700 > Christoph Junghans <jungh...@votca.org> wrote: >> However, I go different route, the input for the coarse-grained >> simulation are mostly rdfs, which you could also calculate using NAMD >> or vmd and feed them into VOTCA and do the coarse-graining >> procedure(IBI/IMC) using VOTCA/gromacs and feed the out-coming >> tabulated interaction back into NAMD. I can help you a bit with the >> middle part or point you to similar setups. > > On Tue, 5 Mar 2013 08:47:52 -0700 > Christoph Junghans <jungh...@votca.org> wrote: >> Is there any special feature you need, which is supported by NAMD, but >> not by Gromacs? Converting simulation inputs from NAMD to Gromacs is >> not very complicated especially for coarse-grained systems. > > -- > Dr. Itsuo HANASAKI > > Assistant Professor > Graduate School of Engineering Science, Osaka University > 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan > E-mail: hanas...@me.es.osaka-u.ac.jp, Phone: +81-6-6850-6179 -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
