Hey, how one can change, for example, after third iteration the numerical parameter and start fourth iteration with a new numerical factor.
cheers, sergii On Jul 15, 2:38 pm, Victor Rühle <[email protected]> wrote: > 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 <[email protected]> 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 of my system (P3HT) divided on the > >> >> >> >> three beads > > > >> and each bead has a different name. > >> >> >> >> How > > ... > > 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.
