Thanks Christoph and Victor. Before I do what you have suggested, I do not know yet 100% how to get both bonded and non-bonded potentials in VOTCA "correctly".
1. For instance, how do you obtain the table.pot file? This file is needed to start the following sequence of commands: csg_sample --in table.pot --out table_resample.pot --grid min:step:max csg_call table extrapolate table_resample.pot table_extrapolate.pot csg_call --options table.xml convert_potential gromacs table_extrapolate.pot table.xvg 2. Similarly, how do I obtain the table.pot for both the bonded and angle potentials which I will resample, extrapolate and later convert to table_b1.xvg and table_a1.xvg? Is the way of obtaining the target non-bonded potentials for the IBI method through force matching (csg_fmatch) or are the potentials only supposed to be derived using csg_stat and/ or csg_boltzmann? Perhaps a step-by-step explanation will help me to reproduce your hexane tutorial and serve to help the other new VOTCA users as well. Thanks a lot. Tinashe On Jan 18, 9:36 pm, Christoph Junghans <[email protected]> wrote: > Hi Tinashe, > > welcome! > > Am 18. Januar 2012 07:18 schrieb Tinashe <[email protected]>:> - 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/votca?hl=en. > > -- > Christoph Junghans > Web:http://www.compphys.de- Hide quoted text - > > - Show quoted text - -- 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.
