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 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 <[email protected]> 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 <[email protected]> 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 to solve it. I > >> >> >> >> >> > > have next error message: > > >> >> >> >> > > "Fatal error: > >> >> >> >> >> > > A tabulated bond interaction table number 2 is out of the table >> range: > >> >> >> >> > > r 0.646802, between table indices 646 and 647, >> table length 501" > > >> >> >> >> >> >> > > Thanks a lot in advance, > >> >> >> >> > > Sergio. > > >> >> >> >> > >> >> > > > On Jun 27, 6:33 pm, Victor Ruehle <[email protected]> wrote: > > >> >> >> > > >> >> >> > > > Hey, > > >> >> >> >> > > > i also use csg_boltzmann, >> >> > > the tab command (dont forget tab set scale > >> >> >> >> > > > bond / >> >> > > tab set scale angle for bond/angles). some of my examples (the > >> >> >> > > >> >> >> > > > .pot files are the output of csg_boltzmann): > >> >> >> >> > > >> >> > > > bonds: > >> >> >> >> > > > cp ../../pot/AB_bond.pot . > >> >> > > >> >> >> >> > > > sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed >> >> > > -e '1,4d' | tac > > >> >> >> >> > > > AB.cut ; cut bad sampled >> >> > > regions at the boundaries > >> >> >> >> > > > csg_call table smooth >> >> > > AB.cut AB.smooth > >> >> >> >> > > > csg_resample --in AB.smooth >> >> > > --out AB.refined --grid 0::0.001:0.5 > >> >> >> ... >> >> 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. 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