2011/7/16 chemistry <[email protected]>: > 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." We do not support something like this. It is not hard to implement it, but things like this are better done by hand anyway.
1.) Do 3 iterations 2.) Change the scale factor 3.) Do more iterations Cheers, Christoph > > 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. > > -- Dr. Christoph Junghans Votca Core Developer Web: http://www.votca.org -- 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.
