Sorry, it was a problem with the internet and that's why I posted the
same message twice.
I'm doing it in the same way how you wrote. So, I'll check all stuff
again and thanks for fast answer.
Kind regards.
On Jul 1, 11:14 am, chemistry <donets1...@gmail.com> wrote:
> Hello!
>
> Seems that I have not a good initial CG-structure. I've got it with
> the help of csg_map:
>
> $csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro
>
> In my mappin.xml file every monomer of my system (P3HT) divided on the
> three beads and each bead has a different name.
> How exactly did you get initial CG-structure for propene in your
> example?
>
> Thanks a lot in advance,
> Sergio
>
> On Jun 30, 12:20 pm, Sebastian <frit...@mpip-mainz.mpg.de> wrote:
>
> > Hi 'chemistry',
>
> > it seems your bond is streching to far, this could be due to a too
> > weak minimum in the bonded interaction or beacause your system
> > explodes (too high energies) in some other part of the system.
> > I would try:
> > 1) run a steepest decent before the actual simulation
> > 2) make the bonded table longer by filling up some zeroes. Then check
> > if something else breaks (with a 'out of range') error....
>
> > -Sebastian
>
> > On Jun 30, 10:34 am, chemistry <donets1...@gmail.com> wrote:
>
> > > Hello!
>
> > > Thanks again for advices. It's helped me a lot.
> > > I have already created all files what I need for CG calculation. But
> > > now I have a problem with a tabulated bond interaction. I've checked
> > > already this problem on the gromacs mailing-list. Unfortunately they
> > > do not have any good advice there how to solve this problem. I would
> > > be very grateful if you can give me some advice how to solve it. I
> > > have next error message:
>
> > > "Fatal error:
> > > A tabulated bond interaction table number 2 is out of the table range:
> > > r 0.646802, between table indices 646 and 647, table length 501"
>
> > > Thanks a lot in advance,
> > > Sergio.
>
> > > On Jun 27, 6:33 pm, Victor Ruehle <rue...@votca.org> wrote:
>
> > > > Hey,
>
> > > > i also use csg_boltzmann, the tab command (dont forget tab set scale
> > > > bond / tab set scale angle for bond/angles). some of my examples (the
> > > > .pot files are the output of csg_boltzmann):
> > > > bonds:
> > > > cp ../../pot/AB_bond.pot .
> > > > sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed -e '1,4d' | tac >
> > > > AB.cut ; cut bad sampled regions at the boundaries
> > > > csg_call table smooth AB.cut AB.smooth
> > > > csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5
> > > > csg_call table extrapolate --function quadratic AB.refined AB.pot.cur
> > > > csg_call --ia-type bonded --ia-name AB --options ../convert.xml
> > > > convert_potential gromacs
>
> > > > angles:
> > > > cp ../../pot/ABC_angle.pot .
> > > > #sed -e '1,3d' -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,3d' | tac >
> > > > ABC.cut
> > > > sed -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,2d' | tac > ABC.cut
> > > > csg_call table smooth ABC.cut ABC.smooth
> > > > csg_resample --in ABC.smooth --out ABC.refined --grid
> > > > 0::0.001:3.141592654
> > > > csg_call table extrapolate --function quadratic --region left
> > > > ABC.refined ABC.refined
> > > > csg_call table extrapolate --function linear --region right
> > > > ABC.refined ABC.refined
> > > > awk '{print $1/3.141592654*180.0,$2}' ABC.refined > ABC.pot.cur
> > > > csg_call --ia-type angle --ia-name ABC --options ../convert.xml
> > > > convert_potential gromacs
>
> > > > convert.xml:
> > > > <cg>
> > > > <bonded>
> > > > <name>AB</name>
> > > > <inverse>
> > > > <gromacs>
> > > > <table>../tables/table_b0.xvg</table>
> > > > </gromacs>
> > > > </inverse>
> > > > </bonded>
> > > > <bonded>
> > > > <name>BC</name>
> > > > <inverse>
> > > > <gromacs>
> > > > <table>../tables/table_b1.xvg</table>
> > > > </gromacs>
> > > > </inverse>
> > > > </bonded>
> > > > <angle>
> > > > <name>ABC</name>
> > > > <inverse>
> > > > <gromacs>
> > > > <table>../tables/table_a0.xvg</table>
> > > > </gromacs>
> > > > </inverse>
> > > > </angle>
>
> > > > <inverse>
> > > > <gromacs>
> > > > <table_end>3.0</table_end>
> > > > <table_bins>0.002</table_bins>
> > > > <pot_max>1000000</pot_max>
> > > > </gromacs>
> > > > </inverse>
> > > > </cg>
>
> > > > Diheral i currently don't have tabulated one (fitted functional form
> > > > in my case), but should be similar.
>
> > > > Best,
> > > > Victor
>
> > > > 2011/6/27 chemistry <donets1...@gmail.com>:
>
> > > > > In this case I have to multiply x value (rad) on (180/3.14) and
> > > > > afterwords I can use this distribution function for getting the
> > > > > potential and if it's not zero just simply shift it to zero?
>
> > > > > On Jun 27, 3:20 pm, Christoph Junghans <jungh...@votca.org> wrote:
> > > > >> You can shift the minimum to zero, it will not change the simulation
> > > > >> result (except for a energy offset).
> > > > >> In VOTCA 1.2 the shifting is done automatically if you are using
> > > > >> 'csg_call convert_potential gromacs'
>
> > > > >> Notice that for angles csg_boltzmann calculates everything in rad,
> > > > >> while gromacs (xvg files) wants degrees, so double check the scale of
> > > > >> the x values again.
>
> > > > >> Cheers,
>
> > > > >> Christoph
>
> > > > >> 2011/6/27 chemistry <donets1...@gmail.com>:
>
> > > > >> > I calculated the potential with awk and with csg_boltzmann. It
> > > > >> > gives
> > > > >> > the same shape of the curves but in the case when I used awk the
> > > > >> > minimum of the potential has negative value. Should I shift the
> > > > >> > minimum of the potential to zero? Does csg_boltzmann do it
> > > > >> > automatically?
>
> > > > >> > Thanks a lot in advance,
> > > > >> > Sergio
>
> > > > >> > On Jun 26, 4:42 pm, Christoph Junghans <jungh...@votca.org> wrote:
> > > > >> >> Hi Sergio,
>
> > > > >> >> the potentials have to look similar around the minimum. The region
> > > > >> >> left and right are usually extrapolated and the exact form of the
> > > > >> >> extrapolation does not matter much as the appearance of these
> > > > >> >> values
> > > > >> >> is exponentially suppressed (exp -E/k_bT).
> > > > >> >> Make sure that the area {U_min..U_min+k_b T} is correct.
>
> > > > >> >> Technically what I do to obtain table_b1.xvg is:
> > > > >> >> -calculate the distribution with csg_stat / csg_boltzmann
> > > > >> >> -calculate the potential using awk
> > > > >> >> $ awk -v kbt=NUMBER '{print $1,($1>0)?-kbt*log($2/$1/$1):"nan"}'
> > > > >> >> bond.dist.new > bond.pot.new
> > > > >> >> -take a look at the potential and cut it down to the well-sampled
> > > > >> >> region
> > > > >> >> -convert it to gromacs format (this was reworked in VOTCA 1.2,
> > > > >> >> before
> > > > >> >> the extrapolation had to be done by hand)
> > > > >> >> $ csg_call --options bond.xml --ia-type bonded convert_potential
> > > > >> >> gromacs bond.pot.new2 table_b1.xvg
> > > > >> >> where bond.xml looks like this:
> > > > >> >> <cg>
> > > > >> >> <inverse>
> > > > >> >> <program>gromacs</program>
> > > > >> >> <gromacs>
> > > > >> >> <pot_max>1e8</pot_max>
> > > > >> >> <table_end>3</table_end>
> > > > >> >> <table_bins>0.002</table_bins>
> > > > >> >> </gromacs>
> > > > >> >> </inverse>
> > > > >> >> </cg>
>
> > > > >> >> table.xvg is used to calculate the interactions for all pairs,
> > > > >> >> which
> > > > >> >> do not appear in energygrp_table (in the mdp file).
> > > > >> >> If all pairs are covered by energygrp_table combinations you can
> > > > >> >> use
> > > > >> >> any table, but I would use a table filled with zeros.
> > > > >> >> table.xvg can be useful in cases when you want to mix IBI tables
> > > > >> >> with
> > > > >> >> a standard force field, then table.xvg should be the default
> > > > >> >> 6-12 LJ
> > > > >> >> table ($GMXDATA/gromacs/top/table6-12.xvg)
>
> > > > >> >> Cheers,
>
> > > > >> >> Christoph
>
> > > > >> >> 2011/6/26 chemistry <donets1...@gmail.com>:
>
> > > > >> >> > Thanks a lot for the previous advices!
>
> > > > >> >> > I have one more question about table_*.xvg. Can you explain
> > > > >> >> > please how
> > > > >> >> > exactly did you create all tables for the propane which you
> > > > >> >> > used for
> > > > >> >> > the ibi-procedure (table.xvg, table_a1.xvg, table_b1.xvg). I
> > > > >> >> > did the
> > > > >> >> > post-processing of the potentials (bond and angle) and I've got
> > > > >> >> > the
> > > > >> >> > same shape for the potentials but much more higher value for
> > > > >> >> > the y-
> > > > >> >> > axis. The distribution functions and potentials for bond and
> > > > >> >> > angle are
> > > > >> >> > the same like in your presentation. Did I do something wrong
> > > > >> >> > or is it
> > > > >> >> > something else what I should know? And which role plays
> > > > >> >> > table.xvg in
> > > > >> >> > this case?
>
> > > > >> >> > Thanks a lot in advance,
> > > > >> >> > Sergio.
>
> > > > >> >> > On Jun 23, 11:34 am, Christoph Junghans <jungh...@votca.org>
> > > > >> >> > wrote:
> > > > >> >> >> Hi Sergio,
>
> > > > >> >> >> 2011/6/22 chemistry <donets1...@gmail.com>:> Thanks a lot for
> > > > >> >> >> advice, I checked all again and I found the mistake
> > > > >> >> >> > in my mappin.xml file. I fixed it and now it works well.
> > > > >> >> >> > Is it something important in the calculation of the rdf in
> > > > >> >> >> > the
> > > > >> >> >> > iterations for such a systems?
>
> > > > >> >> >> Usually one don't want to consider pairs of beads, which
> > > > >> >> >> interact via
> > > > >> >> >> a bonded potential, for the rdf.
> > > > >> >> >> The reason is that the rdf is used to calculate the non-bonded
> > > > >> >> >> interaction and so only the pairs which interact non-bonded
> > > > >> >> >> should go
> > > > >> >> >> in the rdf.
>
> > > > >> >> >> However in some cases it is useful to calculate the rdf with
> > > > >> >> >> different
> > > > >> >> >> exclusions than the simulation was performed. (the
> > > > >> >> >> cg.inverse.gromacs.rdf.topol option in the xml setting file,
> > > > >> >> >> see the
> > > > >> >> >> manual)
>
> > > > >> >> >> Cheers,
>
> > > > >> >> >> Christoph
>
> > > > >> >> >> > Thanks a lot in advance.
> > > > >> >> >> > Sergio
>
> > > > >> >> >> > On Jun 21, 6:02 pm, Victor Ruehle <rue...@votca.org> wrote:
> > > > >> >> >> >> Hmm, are you sure that all the beads which should be
> > > > >> >> >> >> excluded are
> > > > >> >> >> >> part of an angle definition? If yes, Votca should exclude
> > > > >> >> >> >> them
>
> ...
>
> read more »
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