Hey,
Hard to tell what's going wrong, I think you have to play a bit with
it. Maybe first try without pressure correction (remove pressure in
post_update).
cheers,
victor
On Jul 15, 1:52 pm, chemistry <donets1...@gmail.com> wrote:
> Hey!
>
> In general i'm trying to reproduce the article ("Coarse-grained
> computer simulations of polymer/fullerene bulk heterojunctions for
> organic photovoltaic applications", J.Chem.Theory.Comput., Vol.6, No.
> 2, 2010) to be familiar with the ibi procedure. With the help of VOTCA
> I've got all bonded interaction potentials, but i still have a problem
> with getting the non-bonded interaction potentials. I have the same
> RDFs like in this article. During the first three iterations CG
> potentials going down from the initial guess to the desired value, but
> after third-fifth iteration it going up and diverge. The scale
> parameter seems to be just change how fast or how slow it will
> diverge. Is it something else how one can influence on the
> convergency?
>
> Thanks a lot in advance,
> Sergio
>
> On Jul 12, 5:28 pm, Christoph Junghans <jungh...@votca.org> wrote:
>
>
>
>
>
>
>
> > You forget adding "scale" to the "post_update" list.
>
> > Cheers,
>
> > Christoph
>
> > 2011/7/12 chemistry <donets1...@gmail.com>:
>
> > > Hey!
>
> > > Can you please explain how exactly I can set and variate numerical
> > > factor ai (0<ai<1) for U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)).
> > > Because after 10 iteration instead of convergence I have a big
> > > divergence. I've specified already simple pressure correction and it
> > > works:
> > > <cg>
> > > ...
> > > <inverse>
> > > <p_target>1</p_target>
> > > <post_update>pressure</post_update>
> > > <post_update_options>
> > > <pressure>
> > > <do>0 0 1</do>
> > > <type>simple</type>
> > > <simple>
> > > <scale>0.0003</scale>
> > > </simple>
> > > </pressure>
> > > </post_update_options>
>
> > > Which update script I should use for this purpose and in which section
> > > of settings.xml file I need to specify this option?
>
> > > Thanks a lot in advance,
> > > Sergio.
>
> > > On Jul 10, 8:12 pm, "Victor Rühle" <rue...@votca.org> wrote:
> > >> Use the post update script scale and its corresponding option
>
> > >>http://www.votca.org/Documentation/reference-cginteraction
> > >> --
> > >> Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail
> > >> gesendet.
>
> > >> chemistry <donets1...@gmail.com> schrieb:
>
> > >> Hello! in U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)) where one can set
> > >> numerical factor ai (0<ai<1). At the moment my calculation is diverges,
> > >> so in general how one can reach better convergency? Kind regards, Sergio
> > >> On Jul 7, 5:03 pm, Christoph Junghans <jungh...@votca.org> wrote: >
> > >> 2011/7/7 chemistry <donets1...@gmail.com>:> Is it possible do not use
> > >> tables_*.xvg and instead of it set the > > parameters for bond, angle
> > >> and dihedral to the topol.top with > > equilibrium bond length, angle
> > >> and force constants. In this case ibi- > > procedure for my system
> > >> works. > > Yes, if the potential can be reasonably approximated by a
> > >> harmonic > form. Just compare the table to k/2*(r-r_0)^2 ! > > > And how
> > >> one can choose the exact simulation time for one iteration for > >
> > >> different systems? > > There is no rule. The iteration has to be long
> > >> enough, so that the > distributions of the interactions, you want to
> > >> iteratively refine, are > sampled reasonable. Too long iterations just
> > >> waste your computer
> > >> time > ;-) > I usually do 100 short iterations follow by 50 longer ones,
> > >> but that > is my personal recipe. > > Cheers, > > Christoph > > > > >
> > >> Thanks a lot in advance, > > Sergio > > > On Jul 5, 5:04 pm, Victor
> > >> Ruehle <rue...@votca.org> wrote: > >> Hey, > > >> 1) I recommend to use
> > >> version 1.2. The functionality + arguments of > >> convert_potentials
> > >> have slightly changed. > > >> 2) in the files you sent me, the bad
> > >> sampled regions were not cut and > >> therefore the extrapolate failed
> > >> (zoom in at table_a0.xvg where the > >> extrapolated region at the left
> > >> starts). This will lead to a very > >> strong peak in the force and is
> > >> probably what messes up your run. > >> Please make sure to really cut
> > >> the very rough points at the left and > >> right of bonded potentials.
> > >> This was done in the sed commands i send > >> you. Either adjust the
> > >> number of points there or better skip this > >> command and do it
> > >> manually. > > >> Victor > > >> 2011/7/5 chemistry
> > >> <donets1...@gmail.com>: > > >> > Hey,> > >> > the format of the
> > >> table_*.xvg which was created after post-processing > >> > looks like
> > >> this: > > >> > table_a1.xvg: > > >> > 0.0000000000e+00
> > >> 8.6955642509e+07 0.0000000000e+00 > >> > 5.0000000000e-02
> > >> 8.6862417509e+07 1.8640000000e+06 > >> > 1.0000000000e-01
> > >> 8.6769242509e+07 1.8630000000e+06 > >> > 1.5000000000e-01
> > >> 8.6676117509e+07 1.8620000000e+06 > >> > 2.0000000000e-01
> > >> 8.6583042509e+07 1.8610000000e+06 > > >> > and yesterday I've created
> > >> the same format of the table like in your > >> > case by myself. I used
> > >> for this C-programing and described the > >> > potential with the help
> > >> of harmonic potential. And now it works well. > > >> > new one
> > >> table_a1.xvg: > > >> > 0.000000 1201.461834 0 > >> > 0.050000
> > >> 1200.343519 0 > >> > 0.100000 1199.225724 0 > >> > 0.150000 1198.108451
> > >> 0 > >> > 0.200000 1196.991698 0 > > >> > In both cases the potentials
> > >> look similar around the minimum. Is it > >> > possible that the GROMACS
> > >> in someway cannot read correctly the > >> >
>
> > >> table_*.xvg? > > >> > Kind regards, > >> > Sergio > > >> > On Jul 4,
> > >> 7:50 pm, Victor Ruehle <rue...@votca.org> wrote: > >> >> Hey, > > >> >>
> > >> can you please attach your table_?.xvg > > >> >> Cheers, > >> >> Victor
> > >> > > >> >> 2011/7/4 chemistry <donets1...@gmail.com>: > > >> >> > Hey,
> > >> Victor! > > >> >> > With table_b1.xvg and table_a1.xvg from your
> > >> tutorial simulation for > >> >> > propane works well. > >> >> > I'd
> > >> tried to process the potentials for propane myself and after when > >>
> > >> >> > I started the simulations I've got the same mistake like for my >
> > >> >> >> > system: > > >> >> > "Fatal error: > >> >> > A tabulated bond
> > >> interaction table number 1 is out of the table range: > >> >> > r
> > >> 3.157974, between table indices 3157 and 3158, table length 501" > > >>
> > >> >> > Seems that I have some problem with creating the tables_*.xvg > >>
> > >> >> > Can you please check the way of post-processing of the potentials.
> > >> > >> >> > At the beginning I had the same shape of the potential like in
> > >> your > >> >> >
> > >> case (I've got it with csg_boltzmann from all-atom MD simulation of > >>
> > >> >> > propane at T=200 K): > > >> >> > bond: > > >> >> > sed -e '1,5d' -e
> > >> 's/$/ i/' AB.pot | tac | sed -e '1,4d' | tac > AB.cut > >> >> > csg_call
> > >> table smooth AB.cut AB.smooth > >> >> > csg_resample --in AB.smooth
> > >> --out AB.refined --grid 0::0.001:0.5 > >> >> > csg_call table
> > >> extrapolate --function quadratic AB.refined AB.pot.cur > >> >> >
> > >> csg_call --options table.xml convert_potential xvg --type bonded > >> >>
> > >> > AB.pot.cur table_b1.xvg > > >> >> > where table.xml: > > >> >> > <cg>
> > >> > >> >> > <inverse> > >> >> > <gromacs> > >> >> >
> > >> <pot_max>1e8</pot_max> > >> >> > <table_end>0.5</table_end> > >> >>
> > >> > <table_bins>0.002</table_bins> > >> >> > </gromacs> > >> >> >
> > >> </inverse> > >> >> > </cg> > > >> >> > angle: > > >> >> > sed -e 's/$/
> > >> i/' ABA_angle.pot | tac | sed -e '1,2d' | tac > ABA.cut > >> >> > awk
> > >> '{print $1/3.141592654*180.0,$2,$3,$4}' ABA.cut > ABA.new.cut > >> >> >
> > >> csg_call table
> > >> smooth ABA.new.cut ABA.smooth > >> >> > csg_resample --in ABA.smooth
> > >> --out ABA.refined --grid 0::0.05:180 > >> >> > csg_call table
> > >> extrapolate --function quadratic ABA.refined > >> >> > ABA.pot.cur > >>
> > >> >> > csg_call --options table.xml convert_potential xvg --type bonded >
> > >> >> >> > ABA.pot.cur table_a1.xvg > > >> >> > where table.xml: > > >> >>
> > >> > <cg> > >> >> > <inverse> > >> >> > <gromacs> > >> >> >
> > >> <pot_max>1e8</pot_max> > >> >> > <table_end>180</table_end> > >> >>
> > >> > <table_bins>0.05</table_bins> > >> >> > </gromacs> > >> >> >
> > >> </inverse> > >> >> > </cg> > > >> >> > In both cases the potentials look
> > >> similar around the minimum, but > >> >> > afterwords they are totally
> > >> different. I wanted to get the same > >> >> > table_*.xvg like in your
> > >> example. > > >> >> > Yours respectfully, > >> >> > Sergio > > >> >> > On
> > >> Jul 1, 11:34 am, Victor Ruehle <rue...@votca.org> wrote: > >> >> >> Be
> > >> aware, if you have a bug in your coarse-grained topology, it might > >>
> > >> >> >>
> > >> immediately crash the simulations similar to the problem you > >> >> >>
> > >> described. The csg_map will give a reasonable initial structure, this >
> > >> >> >> >> should do well if your coarse-grained potentials are ok
> > >> (eventually do > >> >> >> a steep before). The topology generation
> > >> (csg_gmxtopol) just provides > >> >> >> a point to start from but will
> > >> always require tuning by hand to put in > >> >> >> correct parameters. >
> > >> > >> >> >> Also verify your mapping by loading atomistic +
> > >> coarse-grained > >> >> >> structures in vmd. > > >> >> >> 2011/7/1
> > >> chemistry <donets1...@gmail.com>: > > >> >> >> > 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...
>
> read more »
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