Hi, In my case i have the similar shape of the RDFs coming from the iterations to the reference RDFs. But the RDFs coming from the iterations do not converge to the reference RDFs, that's why i want to try to change the numerical factor (0<ai<1) during the iterations, maybe it will help to reach needed value of the potential. And back to my previous question: "how one can change, for example, after third iteration the numerical parameter and start fourth iteration with a new numerical factor."
Thanks a lot in advance, Sergio. On Jul 15, 2:49 pm, Dominik Fritz <[email protected]> wrote: > 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 <[email protected]> wrote: > > >> You forget adding "scale" to the "post_update" list. > > >> Cheers, > > >> Christoph > > >> 2011/7/12 chemistry <[email protected]>: > > >>> 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" <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: > > >>>> 2011/7/7 chemistry <[email protected]>:> 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 <[email protected]> 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 > >>>> <[email protected]>: > > >> > 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 <[email protected]> wrote: > >> >> Hey, > > >> >> > >>>> can you please attach your table_?.xvg > > >> >> Cheers, > >> >> Victor > >>>> > > >> >> 2011/7/4 chemistry <[email protected]>: > > >> >> > 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 <[email protected]> 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 <[email protected]>: > > >> >> >> > 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 > >>>> <[email protected]> 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 > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
