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 >> >> > >> >> > >> >> > 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.
