W dniu poniedziałek, 1 lipca 2013 15:28:35 UTC+1 użytkownik Christoph
Junghans napisał:
>
> 2013/7/1 <s.neu...@gmail.com <javascript:>>:
> >
> >
> > W dniu poniedziałek, 1 lipca 2013 15:04:38 UTC+1 użytkownik Christoph
> > Junghans napisał:
> >>
> >> 2013/7/1 <s.neu...@gmail.com>:
> >> >
> >> >
> >> > W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik Christoph
> >> > Junghans napisał:
> >> >>
> >> >> 2013/6/18 <s.neu...@gmail.com>:
> >> >> > 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?
>
> >
> > 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!
>
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?
Thanks,
Steven
>
> >
> >>
> >> >
> >> > Steven
> >> >
> >> >
> >> >>
> >> >>
> >> >> > Steven
> >> >> >
> >> >> > --
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> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >
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> >> >
> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
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>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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