Am 20. Januar 2012 09:41 schrieb Tinashe <[email protected]>: > 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: I guess, you are speaking about those non-bonded interaction which are not iterated, usually named table.xvg and table_X_Y.xvg in the maindir.
table.xvg is Gromacs standard interaction table for all non-bonded interaction, which are not covered by the pairs listed in energygrp_table of your mdp file. In all examples of csg-tutorial this file has no meaning as all interaction are covered by energygrp_table, so you can fill it with zeros. However gromacs still needs it. (see Gromacs Manual for details) table_X_Y.xvg, where X and Y are groups from energygrps of your mdp file, can come for a former ibi simulation or somewhere else. These are only needed if you do a iteration of only some of the non-bonded interactions, no csg tutorial does that. > > 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? These are bonded interactions. See chapter 5 of the manual on how to calculate them. Basically you do simple Boltzmann inversion using csg_boltzmann or a simple script. > > 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? IBI aims to reproduce distributions (structure based coarse-graining), while force matching aims to reproduce force. csg_stat only calculates bonded and non-bonded distributions. csg_boltzmann calculates bonded distribution and other analysis including Boltzmann inversion. Christoph > > 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. > -- 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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