2013/7/2 <[email protected]>: > > > On Monday, July 1, 2013 5:09:27 PM UTC+1, Christoph Junghans wrote: >> >> 2013/7/1 <[email protected]>: >> > >> > >> > W dniu poniedziałek, 1 lipca 2013 16:27:04 UTC+1 użytkownik Christoph >> > Junghans napisał: >> >> >> >> 2013/7/1 <[email protected]>: >> >> > >> >> > >> >> > W dniu poniedziałek, 1 lipca 2013 15:28:35 UTC+1 użytkownik Christoph >> >> > Junghans napisał: >> >> >> >> >> >> 2013/7/1 <[email protected]>: >> >> >> > >> >> >> > >> >> >> > W dniu poniedziałek, 1 lipca 2013 15:04:38 UTC+1 użytkownik >> >> >> > Christoph >> >> >> > Junghans napisał: >> >> >> >> >> >> >> >> 2013/7/1 <[email protected]>: >> >> >> >> > >> >> >> >> > >> >> >> >> > W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik >> >> >> >> > Christoph >> >> >> >> > Junghans napisał: >> >> >> >> >> >> >> >> >> >> 2013/6/18 <[email protected]>: >> >> >> >> >> > Dear Votca Users, >> >> >> >> >> > >> >> >> >> >> > I have started using the software some time ago and i >> >> >> >> >> > successfully >> >> >> >> >> > managed >> >> >> >> >> > to extract bonded parameters from atomistic into the >> >> >> >> >> > coarse-grained - >> >> >> >> >> > this >> >> >> >> >> > is done. >> >> >> >> >> > i have my peptide made of 90 residues - each residue is one >> >> >> >> >> > bead, >> >> >> >> >> > however I >> >> >> >> >> > wish to have nonbonded parameters for 5 types of beads (A, >> >> >> >> >> > B, >> >> >> >> >> > C, >> >> >> >> >> > D, >> >> >> >> >> > E). >> >> >> >> >> > In >> >> >> >> >> > this case I will group my amino acids into given types of >> >> >> >> >> > beads. >> >> >> >> >> > >> >> >> >> >> > As I can see the input for IBI method is a RDF e.g. A-A, >> >> >> >> >> > A-B, >> >> >> >> >> > B-B, >> >> >> >> >> > etc >> >> >> >> >> > (25 >> >> >> >> >> > in total). From atomistic I will get 90*90/2 = 4050 RDF >> >> >> >> >> > between >> >> >> >> >> > residues. In >> >> >> >> >> > order to get an input for IBI shall I take an average of of >> >> >> >> >> > RDF >> >> >> >> >> > for >> >> >> >> >> > A-A, >> >> >> >> >> > A-B, etc (25 in total) from atomistic (4050 in total)? It >> >> >> >> >> > will >> >> >> >> >> > not >> >> >> >> >> > reproduce >> >> >> >> >> > atomistic in this case of its average. Please, explain and >> >> >> >> >> > advice >> >> >> >> >> > me. >> >> >> >> >> I guess you need to average your 4050 rdf to get 25 averaged >> >> >> >> >> rdfs. >> >> >> >> >> >> >> >> >> >> You could do that with csg_stat or g_rdf if your simulation >> >> >> >> >> was >> >> >> >> >> done >> >> >> >> >> with gromacs. >> >> >> >> >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> >> >> PS: Sorry for the delay, this email slipped under my radar. >> >> >> >> > >> >> >> >> > >> >> >> >> > Thank you. I think I need to calculate rdf between different >> >> >> >> > types >> >> >> >> > specified >> >> >> >> > in Gromacs... however, residues are neighboring so I wish to >> >> >> >> > exclude >> >> >> >> > those >> >> >> >> > interactions. In gromacs g_rdf does not have this option (-cut >> >> >> >> > option >> >> >> >> > will >> >> >> >> > just cut the distance which is incorrect). Would g_stat be able >> >> >> >> > to >> >> >> >> > exclude >> >> >> >> > neighbors from my atomistic? >> >> >> >> For g_rdf, you could use a special index file or create a tpr >> >> >> >> with >> >> >> >> additional exclusion. >> >> >> >> >> >> >> >> In csg_stat you could add bonds (in the mapping xml file) between >> >> >> >> the >> >> >> >> beads, which you want to exclude. >> >> >> >> >> >> >> >> > Another issue: I used BI for angles - I tried refining my >> >> >> >> > potential >> >> >> >> > using >> >> >> >> > VOTCA but it somehow describes it poorly... Does csg_resample >> >> >> >> > use >> >> >> >> > a >> >> >> >> > function >> >> >> >> > to refine it? What kind of function? >> >> >> >> csg_resample uses akima spline by default, but it can also do >> >> >> >> cubic >> >> >> >> spline or linear interpolation. >> >> >> >> >> >> >> >> > I would prefer to refine it my own but no clue how I will then >> >> >> >> > calculate >> >> >> >> > the >> >> >> >> > derivative of those values (3rd column in table)a*.xvg). Would >> >> >> >> > you >> >> >> >> > advise? >> >> >> >> use csg_resample with --type linear and --derivative file option. >> >> >> >> >> >> >> >> Christoph > > > Thanks again Christoph. I tried csg_resample with default akima option and > it work really well. I calculate derivative as well (--derivative). Then I > want to extrapolate it - how Votca will calculate derivatives of > extrapolated function? Shall I use csg_resample after extraplation again and > then export it to Gromacs format? I would extrapolate the potential not the derivatives, see the section in the manual about that. Just use the $csg_call convert_potential gromacs see the manual for details!
> > Steven > > >> >> >> >> > >> >> >> > >> >> >> > Thank you a lot! csg_resample --type linear will use linear >> >> >> > function >> >> >> > which >> >> >> > is not desired... My distributions are made of multiple gaussian >> >> >> > distributions so i guess akima (deafult) option? >> >> >> If you are using the same grid for input and output, the y points >> >> >> won't >> >> >> change. >> >> >> Linear interpolation will just draw lines between the given points. >> >> >> If you have distributions made of multiple Gaussian, why don't you >> >> >> fit >> >> >> multiple Gaussians to it and write the result out as a table again. >> >> > >> >> > >> >> > Thank you. I tried to fit in another software my potential to 6th >> >> > order >> >> > polynomial but results are not promising... which option of csg_stat >> >> > will >> >> > fit it to multiple gaussian? >> >> There is no VOTCA tools doing that, but you could use scipy or gnuplot. >> >> >> >> >> >> >> >> >> >> >> > >> >> >> > Does Votca 1.2.3 supports IBI for bonded or shall I upgarde it to >> >> >> > 1.3 >> >> >> > ? >> >> >> Bonded IBI only works in Votca 1.3! >> >> See: >> >> <https://code.google.com/p/votca/wiki/Installing#Development_Version> >> >> >> >> > >> >> > >> >> > I will upgrade it. For bonded do we provide both distributions and >> >> > potentials in settings? >> >> > >> >> > <cg> >> >> > <bonded> >> >> > <name>angle</name> >> >> > <min>1</min> >> >> > <max>3</max> >> >> > <step>0.05</step> >> >> > <inverse> >> >> > <target>angle.dist1.tgt</target> >> >> > <gromacs> >> >> > <table>table_a1.xvg</table> >> >> > </gromacs> >> >> > </inverse> >> >> > </bonded> >> >> > >> >> > So the input are both refined table_a1.xvg as well as >> >> > angle.dist1.tgt? >> >> > Will >> >> > they be updated every step? >> >> angle.dist1.tgt is the target distribution against which csg_inverse >> >> compares the current distribution, it is never updated. >> >> table_a1.xvg is the table to export VOTCAs internal potential to, it >> >> is updated every iteration step. >> >> >> > Thank you. But for both bonded and nonbonded do I have to have two >> > inputs: >> > distribution and potential? >> > Another issue: are tables*xvg copied every time or shall I add them to >> > the >> > list to be copied? they are not specified in the tutorial as files to be >> > copied: >> > >> > >> > http://code.google.com/p/votca/source/browse/hexane/ibi_bonded/settings.xml?repo=csg-tutorials >> The tables are generated for every interaction, which appears in your >> settings xml file. >> >> The target distributions are the only inputs you need for non-bonded >> interactions. For the bonded interactions you will need an initial >> guesses for the potential in addition (pot.in file). >> >> > >> > Steven >> > >> > >> >> >> >> > >> >> > Thanks, >> >> > >> >> > Steven >> >> > >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> > >> >> >> >> > Steven >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > Steven >> >> >> >> >> > >> >> >> >> >> > -- >> >> >> >> >> > 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 [email protected]. >> >> >> >> >> > To post to this group, send email to [email protected]. >> >> >> >> >> > Visit this group at http://groups.google.com/group/votca. >> >> >> >> >> > For more options, visit >> >> >> >> >> > https://groups.google.com/groups/opt_out. >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> 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 [email protected]. >> >> >> >> > To post to this group, send email to [email protected]. >> >> >> >> > Visit this group at http://groups.google.com/group/votca. >> >> >> >> > For more options, visit >> >> >> >> > https://groups.google.com/groups/opt_out. >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> 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 [email protected]. >> >> >> > To post to this group, send email to [email protected]. >> >> >> > Visit this group at http://groups.google.com/group/votca. >> >> >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> 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 [email protected]. >> >> > To post to this group, send email to [email protected]. >> >> > Visit this group at http://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> > >> >> > >> >> >> >> >> >> >> >> -- >> >> 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 [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> >> >> -- >> 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 [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > -- 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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