Hi Sergio,
have you checked, that you treat intramolecular exclusions in a
consistent way?
When you obtain the reference RDFs, you typically exclude
(intramolecular) pairs of beads, which are interacting via bonded
interactions.
The same exclusions have to be used for the RDFs coming from the
iteration steps; otherwise your potentials will most probably diverge.
Cheers,
Dominik
On 07/15/2011 01:52 PM, chemistry 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 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
>>>>
>> ...
>>
>> read more »
>>
>
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