Hi Tinashe, welcome!
Am 18. Januar 2012 07:18 schrieb Tinashe <tinashe.nd...@gmail.com>: > - the min/max/step values for force matching i get from the > distribution functions, that it samples a valid interval, and the > number of bins is not too high, otherwise might become slow > - the table_a1*.xvg are usually generated using csg_boltzmann, there > is a section in the manual. You can convert the votca potential files > to gromacs using csg_call. I have to lookup the correct command, but > christoph might answer on googlrgroups. See section 4.2 of the manual: <https://votca.googlecode.com/files/votca-csg-manual-1.2.2.pdf> But basically once you have the potential in Votca format, it boils down to the following: -create a simple settings xml file (table.xml): <cg> <inverse> <gromacs> <pot_max>1e8</pot_max> <table_end>8.0</table_end> <table_bins>0.002</table_bins> </gromacs> </inverse> </cg> and run $csg_call --ia-type TYPE --options table.xml convert_potential gromacs \ table_extrapolate.pot table.xvg where type can be non-bonded, bonded, angle, dihedral. Note, that in the current development version we renamed "bonded" to "bond"! Cheers, Christoph > - renaming te distribution function and use it as target is the proper > way to do > - you can make a few optimizations in the grompp, e.g. if you don't > have charge in the cg model, use cut-off as estatic method. this will > disable the fft from pme. > > > Best, > Victor > > >> Dear Victor, >> >> Firstly, thanks a lot, your suggestions were on the mark. >> >> At first, I ran the following command: >> csg_stat --top topol.tpr --trj traj.trr --cg hexane.xml --nt 3 --options >> fmatch.xml >> and then renamed the files from *.dist.new to *.dist.tgt to use together >> with the settings file. Is this the correct way to things? >> >> How are the following files meant to be created: table.xvg table_a1.xvg >> table_b1.xvg >> Where does one get the numbers in the settings.xml and fmatch.xml? I have >> simply used numbers from VOTCA tutorials? >> It appears that I can still use the same grommp file as the one I used for >> atomistic simulations, is this so? >> >> Kind regards, >> Tinashe > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to votca@googlegroups.com. > To unsubscribe from this group, send email to > votca+unsubscr...@googlegroups.com. > 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 votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
