2013/7/25 <[email protected]>: > > > On Wednesday, July 24, 2013 8:56:13 PM UTC+1, Christoph Junghans wrote: >> >> 2013/7/24 <[email protected]>: >> > My apologies, I am sorry for this but been fighting a long time with >> > this. >> > >> > I wish I could use bonds as you mentioned but I have 90 beads divided >> > into 5 >> > groups (15 potentials) and they are in different places. Some groups >> > have 28 >> > beads and some have 2 beads. I do not think it is possible to make >> > tabulated >> > bonds between those groups. >> > >> > As you mentioned the problem is with the input file - RDFs. My RDF does >> > not >> > correspond to those calculated by Votca or Gromacs. I prodcued and >> > refined >> > them on my own and then created NAME.pot.in as an input. So after each >> > step >> > Votca calculates distributions which are correct (but wrong in my case >> > as I >> > changed them). Then dividing new distribution over the target gives a >> > garbage. Would you please recommend something in that case? Or I have to >> > make each iteration manually? >> What is the definition of your RDF? If it is not too hard, you might >> be able to modify csg_stat, so that it calculates the rdf differently. >> An option would be to write scripts, which overwrites the default rdf >> calculation: >> - create a folder "scripts" >> - add that directory to cg.inverse.scriptdir in your xml file >> - create a file csg_table with the following line >> rdf gromacs my_rdf.sh >> - get the default rdf calculation script: >> $ csg_call --show rdf gromacs >> - same it under the name my_rdf.sh >> - modify my_rdf.sh > > > > Thank you. I just need option -fade VALUE in g_rdf (after this value RDF > goes to 1) to use it instead of using csg_stat. My results are messed up > just beacuse csg_stat provides distributions which goes to zero. Can I use > somehow in my xml file: > > <gromacs> > <g_rdf> > <opts> -fade VALUE </opts> > </g_rdf> > </gromacs> We don't use g_rdf to calculate the rdfs, you will have to create a custom rdf calculation for that.
Another option would be to add a fade option to csg_stat, which isn't very hard: g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 for r>=fade Right? > > ??? > > Steven > >> >> > >> > Steven >> > >> > >> > On Wednesday, July 24, 2013 5:22:01 PM UTC+1, Christoph Junghans wrote: >> >> >> >> 2013/7/24 <[email protected]>: >> >> > >> >> > >> >> > W dniu środa, 24 lipca 2013 13:36:04 UTC+1 użytkownik >> >> > [email protected] >> >> > napisał: >> >> >> >> >> >> I am also trying to iteratively get distribution for 1 of my >> >> >> interactions >> >> >> leaving other 14 being fully repulsive.... My potential at step 124 >> >> >> has >> >> >> a >> >> >> much deeper minima than the initial one... And ditribution is much >> >> >> higher >> >> >> than the target one obviously... These beads of which potential i am >> >> >> trying >> >> >> to get stay in a globular conformation...There must be something >> >> >> wrong.. >> >> >> Please, see attached my files, any help appreciated. >> >> >> >> >> >> Steven >> >> >> >> >> > >> >> > It is absolutely ridiculous... I used the cut off of 0.4 to refine >> >> > this >> >> > one >> >> > potential as a trial and with comparing to my target distribution it >> >> > was >> >> > underestimated... so what Votca did? Exactly opposite... I looked at >> >> > the >> >> > next steps and the distributions are even smaller...!!! Fantastic! >> >> This was your 1st strike out of three. Please clam down and mind your >> >> words! >> >> >> >> So far you have never been able to show me that VOTCA did something >> >> wrong. Like for all other simulation packages, for VOTCA the >> >> garbage-in-garbage-out principle applies, too. VOTCA is deterministic, >> >> it can only handle inputs it was made for and it cannot make >> >> scientific decisions for you. If you give it unexpected input >> >> ("garbage"), it will most likely not turn it into gold. >> >> >> >> Btw. VOTCA is open-source, if you don't like how it is working, feel >> >> free to change the code. (but remember to call your derived code >> >> differently!) >> >> >> >> Victor, Tristan, Sikandar, me and all the other developers are >> >> providing technical support on a voluntary and free of charge basis. >> >> >> >> All that said, let's come back to your question. >> >> >> >> The target distribution distribution is something you give as an >> >> input, VOTCA does nothing else than putting is on the same grid as the >> >> interaction and even that can be prevented if you provide it with the >> >> right grid already. To check that compare step_*/NAME.dist.tgt with >> >> whatever you put in the main directory. >> >> >> >> Your distribution looks artificially high and I am not sure where this >> >> is coming from. You could try running g_rdf in one of the step to see >> >> if csg_stat does something wrong, but I doubt that the normalization >> >> is just the standard shell volume: >> >> >> >> >> >> <https://code.google.com/p/votca/source/browse/src/tools/csg_stat_imc.cc?repo=csg&name=stable#383> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> W dniu wtorek, 23 lipca 2013 20:05:45 UTC+1 użytkownik Christoph >> >> >> Junghans >> >> >> napisał: >> >> >>> >> >> >>> 2013/7/23 <[email protected]>: >> >> >>> > >> >> >>> > >> >> >>> > W dniu wtorek, 23 lipca 2013 16:24:25 UTC+1 użytkownik Christoph >> >> >>> > Junghans >> >> >>> > napisał: >> >> >>> >> >> >> >>> >> 2013/7/23 <[email protected]>: >> >> >>> >> > Another example which seems to be correct but wish to know, >> >> >>> >> > please >> >> >>> >> > see >> >> >>> >> > attached. The derivative (last column) of function H(x) is >> >> >>> >> > zero >> >> >>> >> > while >> >> >>> >> > H(x) >> >> >>> >> > is highly positive... Is that correct potential? >> >> >>> >> I don't see a problem here, the begin of the potential is >> >> >>> >> constant >> >> >>> >> and >> >> >>> >> hence the derivative is zero. >> >> >>> >> >> >> >>> >> > My protein still stays in a >> >> >>> >> > globular conformation and I corrected other potentials. If it >> >> >>> >> > is >> >> >>> >> > ok >> >> >>> >> > would >> >> >>> >> > you try to make IBI with potentials one by one? >> >> >>> >> do_potential in the xml file allows you to divide interactions >> >> >>> >> into >> >> >>> >> group to update only one group at the time. >> >> >>> >> The default will put all interactions in one group. >> >> >>> >> >> >> >>> >> I would approximate your 4 special interactions by a non-linear >> >> >>> >> spring-like potential (see my earlier email) and keep them fixed >> >> >>> >> for >> >> >>> >> now and do IBI on the other 11 interactions. >> >> >>> > >> >> >>> > >> >> >>> > The problem is that all 15 of my distributions goes to zero as >> >> >>> > there >> >> >>> > is >> >> >>> > nothing at large distances. I already have angles take from >> >> >>> > atomistic >> >> >>> > simulations, by one boltzmann inversion I got great results >> >> >>> > (tabulated >> >> >>> > angles). Now I shifted my distributions to RDF = 1 which option >> >> >>> > 1. >> >> >>> > Then >> >> >>> > I >> >> >>> > should use: >> >> >>> > for the 1st potential >> >> >>> > potentia.update 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >> >> >>> > for the second >> >> >>> > potential.update 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 >> >> >>> > etc. am I right? >> >> >>> Yes! >> >> >>> >> >> >>> > >> >> >>> > The other option would be to to use the non-linear spring as for >> >> >>> > bonded >> >> >>> > (you >> >> >>> > mentioned before). Does only Votca 1.3 supports it? Is there any >> >> >>> > tutorial? >> >> >>> > Which option would you recommend? >> >> >>> I meant to Boltzmann invert the distribution and use it as >> >> >>> table_bX.xvg and keep it fixed. >> >> >>> But it will depend on your system if this approach will work or >> >> >>> not. >> >> >>> >> >> >>> >> >> >>> > >> >> >>> > Steven >> >> >>> > >> >> >>> > >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> > >> >> >>> >> > Steven >> >> >>> >> > >> >> >>> >> > W dniu wtorek, 23 lipca 2013 10:22:26 UTC+1 użytkownik >> >> >>> >> > [email protected] >> >> >>> >> > napisał: >> >> >>> >> >> >> >> >>> >> >> Could you please also explain me why from attached potential >> >> >>> >> >> Votca >> >> >>> >> >> produce >> >> >>> >> >> a table with negative (close to zero) values at low >> >> >>> >> >> distances? >> >> >>> >> >> It >> >> >>> >> >> does >> >> >>> >> >> not >> >> >>> >> >> make sense and hence my protein remains globular... I have 4 >> >> >>> >> >> potentials >> >> >>> >> >> like >> >> >>> >> >> this out of 15... >> >> >>> >> >> >> >> >>> >> >> Steven >> >> >>> >> >> >> >> >>> >> >> W dniu poniedziałek, 22 lipca 2013 23:40:50 UTC+1 użytkownik >> >> >>> >> >> Christoph >> >> >>> >> >> Junghans napisał: >> >> >>> >> >>> >> >> >>> >> >>> 2013/7/22 <[email protected]>: >> >> >>> >> >>> > >> >> >>> >> >>> > >> >> >>> >> >>> > On Friday, July 19, 2013 8:02:01 PM UTC+1, Christoph >> >> >>> >> >>> > Junghans >> >> >>> >> >>> > wrote: >> >> >>> >> >>> >> >> >> >>> >> >>> >> 2013/7/19 <[email protected]>: >> >> >>> >> >>> >> > Thank you for this. >> >> >>> >> >>> >> > I recalculated my distributions and make them a value >> >> >>> >> >>> >> > between >> >> >>> >> >>> >> > 0 >> >> >>> >> >>> >> > and >> >> >>> >> >>> >> > 1 at >> >> >>> >> >>> >> > large distances. If I submit then my own potential >> >> >>> >> >>> >> > pot.in >> >> >>> >> >>> >> > which >> >> >>> >> >>> >> > goes >> >> >>> >> >>> >> > to >> >> >>> >> >>> >> > a >> >> >>> >> >>> >> > positive value in this case would votca not shift the >> >> >>> >> >>> >> > potential >> >> >>> >> >>> >> > after >> >> >>> >> >>> >> > each >> >> >>> >> >>> >> > iteration to zero? Please, let me know. >> >> >>> >> >>> >> VOTCA always shifts the potential, to U(r_max)=0 for >> >> >>> >> >>> >> non-bonded >> >> >>> >> >>> >> interaction and U_min=0 for bonded interactions. >> >> >>> >> >>> >> This is why I said making VOTCA believe your interaction >> >> >>> >> >>> >> is >> >> >>> >> >>> >> bonded, >> >> >>> >> >>> >> might >> >> >>> >> >>> >> help. >> >> >>> >> >>> >> The update rule is the same for bonded and non-bonded. >> >> >>> >> >>> >> >> >> >>> >> >>> >> Anyhow the shift doesn't change the physics, so why are >> >> >>> >> >>> >> you >> >> >>> >> >>> >> so >> >> >>> >> >>> >> bother >> >> >>> >> >>> >> about it? You could just to do IBI and shift the finial >> >> >>> >> >>> >> outcome >> >> >>> >> >>> >> once >> >> >>> >> >>> >> it is converged. >> >> >>> >> >>> >> >> >> >>> >> >>> >> Christoph >> >> >>> >> >>> > >> >> >>> >> >>> > >> >> >>> >> >>> > Thank you. This what I will do - shift the final >> >> >>> >> >>> > potential. >> >> >>> >> >>> > what >> >> >>> >> >>> > would >> >> >>> >> >>> > be >> >> >>> >> >>> > the best cut off for IBI - is that the place where >> >> >>> >> >>> > distributions >> >> >>> >> >>> > have >> >> >>> >> >>> > maxima? >> >> >>> >> >>> That is a tricky question, to be honest I don't know. You >> >> >>> >> >>> might >> >> >>> >> >>> have >> >> >>> >> >>> to play with the cutoff a bit. >> >> >>> >> >>> >> >> >>> >> >>> > >> >> >>> >> >>> > >> >> >>> >> >>> > Steven >> >> >>> >> >>> > >> >> >>> >> >>> > >> >> >>> >> >>> >> >> >> >>> >> >>> >> > >> >> >>> >> >>> >> > Steven >> >> >>> >> >>> >> > >> >> >>> >> >>> >> > W dniu środa, 17 lipca 2013 17:43:51 UTC+1 użytkownik >> >> >>> >> >>> >> > Christoph >> >> >>> >> >>> >> > Junghans >> >> >>> >> >>> >> > napisał: >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> 2013/7/17 <[email protected]>: >> >> >>> >> >>> >> >> > Thank you for this. >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> > Another question - presumably I will specify my own >> >> >>> >> >>> >> >> > distributions >> >> >>> >> >>> >> >> > (not >> >> >>> >> >>> >> >> > from >> >> >>> >> >>> >> >> > VOTCA) with some simplifications. Then I will create >> >> >>> >> >>> >> >> > intial >> >> >>> >> >>> >> >> > potentials >> >> >>> >> >>> >> >> > to >> >> >>> >> >>> >> >> > IBI as name.pot.in. Votca will try to fit to my >> >> >>> >> >>> >> >> > distributions >> >> >>> >> >>> >> >> > to >> >> >>> >> >>> >> >> > the >> >> >>> >> >>> >> >> > one >> >> >>> >> >>> >> >> > submitted in the main directory. However, by >> >> >>> >> >>> >> >> > calculating >> >> >>> >> >>> >> >> > distributions >> >> >>> >> >>> >> >> > after >> >> >>> >> >>> >> >> > each step these will not be distributions which >> >> >>> >> >>> >> >> > could >> >> >>> >> >>> >> >> > possibly >> >> >>> >> >>> >> >> > match >> >> >>> >> >>> >> >> > my >> >> >>> >> >>> >> >> > initial with simpifications, am I right? Do I have >> >> >>> >> >>> >> >> > to >> >> >>> >> >>> >> >> > calculate >> >> >>> >> >>> >> >> > RDFs >> >> >>> >> >>> >> >> > at >> >> >>> >> >>> >> >> > each >> >> >>> >> >>> >> >> > step on my own then? >> >> >>> >> >>> >> >> 1.) If you give VOTCA a pot.in, it will not do use the >> >> >>> >> >>> >> >> potential >> >> >>> >> >>> >> >> of >> >> >>> >> >>> >> >> mean as initial guess in step_000, but just your >> >> >>> >> >>> >> >> potential. >> >> >>> >> >>> >> >> 2.) Independently of pot.in, VOTCA will always compare >> >> >>> >> >>> >> >> dist.new >> >> >>> >> >>> >> >> against dist.tgt every step >> >> >>> >> >>> >> >> 3.) dist.new is calculated in every iteration using >> >> >>> >> >>> >> >> csg_stat, >> >> >>> >> >>> >> >> you >> >> >>> >> >>> >> >> could make VOTCA fit only the part 0 to min. >> >> >>> >> >>> >> >> 3b.) You could write a custom post-update script to do >> >> >>> >> >>> >> >> whatever >> >> >>> >> >>> >> >> rdf >> >> >>> >> >>> >> >> calculation/ potential modification after you want. >> >> >>> >> >>> >> >> This >> >> >>> >> >>> >> >> can >> >> >>> >> >>> >> >> be >> >> >>> >> >>> >> >> used >> >> >>> >> >>> >> >> to overwrite rdf calculated by csg_stat. >> >> >>> >> >>> >> >> 3c.) All of this seems a bit hacky, why don't you just >> >> >>> >> >>> >> >> declare >> >> >>> >> >>> >> >> some >> >> >>> >> >>> >> >> interaction of type bonded, so csg_stat will calculate >> >> >>> >> >>> >> >> p(r)=H(r)/(4pi*r^2) instead of the rdf for those. >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> > Another issue: How Votca normalize RDFs using >> >> >>> >> >>> >> >> > csg_stat >> >> >>> >> >>> >> >> > ? I >> >> >>> >> >>> >> >> > wish >> >> >>> >> >>> >> >> > to >> >> >>> >> >>> >> >> > have >> >> >>> >> >>> >> >> > volume and mass normalized distributions, is that >> >> >>> >> >>> >> >> > possible? >> >> >>> >> >>> >> >> No, we don't have an option to calculate the volume >> >> >>> >> >>> >> >> and >> >> >>> >> >>> >> >> mass >> >> >>> >> >>> >> >> normalized distributions instead. Though it is not >> >> >>> >> >>> >> >> hard >> >> >>> >> >>> >> >> to >> >> >>> >> >>> >> >> implement! >> >> >>> >> >>> >> >> For IBI that would also make no difference as all >> >> >>> >> >>> >> >> normalization >> >> >>> >> >>> >> >> factors drop out in the ratio g(r)/g_target(r) used in >> >> >>> >> >>> >> >> the >> >> >>> >> >>> >> >> update. >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> Christoph >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> > Steven >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> > W dniu wtorek, 16 lipca 2013 23:17:05 UTC+1 >> >> >>> >> >>> >> >> > użytkownik >> >> >>> >> >>> >> >> > Christoph >> >> >>> >> >>> >> >> > Junghans >> >> >>> >> >>> >> >> > napisał: >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> 2013/7/16 <[email protected]>: >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > W dniu wtorek, 16 lipca 2013 08:48:51 UTC+1 >> >> >>> >> >>> >> >> >> > użytkownik >> >> >>> >> >>> >> >> >> > Tristan >> >> >>> >> >>> >> >> >> > Bereau >> >> >>> >> >>> >> >> >> > napisał: >> >> >>> >> >>> >> >> >> >> >> >> >>> >> >>> >> >> >> >> That sounds like what I was hinting at: from >> >> >>> >> >>> >> >> >> >> what I >> >> >>> >> >>> >> >> >> >> understand, >> >> >>> >> >>> >> >> >> >> you're >> >> >>> >> >>> >> >> >> >> simulating a single protein, not a pure liquid >> >> >>> >> >>> >> >> >> >> of >> >> >>> >> >>> >> >> >> >> stuff. >> >> >>> >> >>> >> >> >> >> So >> >> >>> >> >>> >> >> >> >> your >> >> >>> >> >>> >> >> >> >> RDF >> >> >>> >> >>> >> >> >> >> will never go to 1 because there won't be >> >> >>> >> >>> >> >> >> >> anything >> >> >>> >> >>> >> >> >> >> at >> >> >>> >> >>> >> >> >> >> large >> >> >>> >> >>> >> >> >> >> distances. >> >> >>> >> >>> >> >> >> >> Is that the case? If so, more iterations and/or >> >> >>> >> >>> >> >> >> >> better >> >> >>> >> >>> >> >> >> >> initial >> >> >>> >> >>> >> >> >> >> guesses >> >> >>> >> >>> >> >> >> >> won't cut it. >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > Yes, this is the case. I will aproximate the RDFs >> >> >>> >> >>> >> >> >> > so >> >> >>> >> >>> >> >> >> > that >> >> >>> >> >>> >> >> >> > they >> >> >>> >> >>> >> >> >> > go >> >> >>> >> >>> >> >> >> > to >> >> >>> >> >>> >> >> >> > sth >> >> >>> >> >>> >> >> >> > which is non zero. Thank you. >> >> >>> >> >>> >> >> >> non zero will not be enough, it has to be 1 >> >> >>> >> >>> >> >> >> otherwise >> >> >>> >> >>> >> >> >> your >> >> >>> >> >>> >> >> >> potential >> >> >>> >> >>> >> >> >> will still accumulated whatever the value, >> >> >>> >> >>> >> >> >> kT*log(P(r_cut), >> >> >>> >> >>> >> >> >> at >> >> >>> >> >>> >> >> >> the >> >> >>> >> >>> >> >> >> cutoff is. >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> For me the distributions looks more like a >> >> >>> >> >>> >> >> >> something, >> >> >>> >> >>> >> >> >> which >> >> >>> >> >>> >> >> >> could be >> >> >>> >> >>> >> >> >> modeled with a non-linear spring type potential >> >> >>> >> >>> >> >> >> (r-> >> >> >>> >> >>> >> >> >> +/-inf >> >> >>> >> >>> >> >> >> P->inf), >> >> >>> >> >>> >> >> >> where the minimum is a zero. >> >> >>> >> >>> >> >> >> VOTCA could do that for you if declare the >> >> >>> >> >>> >> >> >> interaction >> >> >>> >> >>> >> >> >> as >> >> >>> >> >>> >> >> >> bonded. >> >> >>> >> >>> >> >> >> (VOTCA's definition of non-bonded and bonded might >> >> >>> >> >>> >> >> >> not >> >> >>> >> >>> >> >> >> be >> >> >>> >> >>> >> >> >> taken >> >> >>> >> >>> >> >> >> too >> >> >>> >> >>> >> >> >> strict.) >> >> >>> >> >>> >> >> >> Also from the modeling point of view, it might make >> >> >>> >> >>> >> >> >> sense >> >> >>> >> >>> >> >> >> to >> >> >>> >> >>> >> >> >> have a >> >> >>> >> >>> >> >> >> spring between some beads, which cannot go >> >> >>> >> >>> >> >> >> infinitely >> >> >>> >> >>> >> >> >> apart >> >> >>> >> >>> >> >> >> due >> >> >>> >> >>> >> >> >> to >> >> >>> >> >>> >> >> >> geometry. >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> Anyhow, these are scientific decisions you have to >> >> >>> >> >>> >> >> >> make >> >> >>> >> >>> >> >> >> yourself. >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> Christoph >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > Steven >> >> >>> >> >>> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >>> >> >>> >> >> >> >> On Mon, Jul 15, 2013 at 10:09 PM, >> >> >>> >> >>> >> >> >> >> <[email protected]> >> >> >>> >> >>> >> >> >> >> wrote: >> >> >>> >> >>> >> >> >> >> > Thank you for this. For heterogenous system >> >> >>> >> >>> >> >> >> >> > RDF >> >> >>> >> >>> >> >> >> >> > does >> >> >>> >> >>> >> >> >> >> > not >> >> >>> >> >>> >> >> >> >> > go >> >> >>> >> >>> >> >> >> >> > to >> >> >>> >> >>> >> >> >> >> > 1 >> >> >>> >> >>> >> >> >> >> > but >> >> >>> >> >>> >> >> >> >> > to >> >> >>> >> >>> >> >> >> >> > 0. >> >> >>> >> >>> >> >> >> >> > In this case I guess I need thousands of >> >> >>> >> >>> >> >> >> >> > iterations... >> >> >>> >> >>> >> >> >> >> > The >> >> >>> >> >>> >> >> >> >> > system >> >> >>> >> >>> >> >> >> >> > input >> >> >>> >> >>> >> >> >> >> > are >> >> >>> >> >>> >> >> >> >> > 15 potentials which makes it so complicated. >> >> >>> >> >>> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> > Steven >> >> >>> >> >>> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> > W dniu poniedziałek, 15 lipca 2013 17:44:46 >> >> >>> >> >>> >> >> >> >> > UTC+1 >> >> >>> >> >>> >> >> >> >> > użytkownik >> >> >>> >> >>> >> >> >> >> > Christoph >> >> >>> >> >>> >> >> >> >> > Junghans napisał: >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> 2013/7/15 <[email protected]>: >> >> >>> >> >>> >> >> >> >> >> > Votca is definitely wrong. If you take the >> >> >>> >> >>> >> >> >> >> >> > example of >> >> >>> >> >>> >> >> >> >> >> > maximum >> >> >>> >> >>> >> >> >> >> >> > of >> >> >>> >> >>> >> >> >> >> >> > my >> >> >>> >> >>> >> >> >> >> >> > ACI-ACI.dist.tgt the maximum corresponds to >> >> >>> >> >>> >> >> >> >> >> > 65.555. >> >> >>> >> >>> >> >> >> >> >> > The >> >> >>> >> >>> >> >> >> >> >> > potential >> >> >>> >> >>> >> >> >> >> >> > at >> >> >>> >> >>> >> >> >> >> >> > this >> >> >>> >> >>> >> >> >> >> >> > point should be: W = -2.49435*ln(65.55) = >> >> >>> >> >>> >> >> >> >> >> > -10.433 >> >> >>> >> >>> >> >> >> >> >> > and >> >> >>> >> >>> >> >> >> >> >> > in >> >> >>> >> >>> >> >> >> >> >> > my >> >> >>> >> >>> >> >> >> >> >> > ACI-ACI.dist.pot >> >> >>> >> >>> >> >> >> >> >> > the value corresponds to -16.1 - it is a >> >> >>> >> >>> >> >> >> >> >> > huge >> >> >>> >> >>> >> >> >> >> >> > difference >> >> >>> >> >>> >> >> >> >> >> > and >> >> >>> >> >>> >> >> >> >> >> > that >> >> >>> >> >>> >> >> >> >> >> > is >> >> >>> >> >>> >> >> >> >> >> > why >> >> >>> >> >>> >> >> >> >> >> > my >> >> >>> >> >>> >> >> >> >> >> > further distributions are so huge.... >> >> >>> >> >>> >> >> >> >> >> No, Votca is 100% correct, and does what it >> >> >>> >> >>> >> >> >> >> >> is >> >> >>> >> >>> >> >> >> >> >> supposed >> >> >>> >> >>> >> >> >> >> >> to >> >> >>> >> >>> >> >> >> >> >> do. >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> First, have a look at your ACI-ACI.dist.tgt >> >> >>> >> >>> >> >> >> >> >> again, >> >> >>> >> >>> >> >> >> >> >> this >> >> >>> >> >>> >> >> >> >> >> distribution >> >> >>> >> >>> >> >> >> >> >> doesn't go to one hence the potential doesn't >> >> >>> >> >>> >> >> >> >> >> go >> >> >>> >> >>> >> >> >> >> >> to >> >> >>> >> >>> >> >> >> >> >> 0 >> >> >>> >> >>> >> >> >> >> >> for >> >> >>> >> >>> >> >> >> >> >> large >> >> >>> >> >>> >> >> >> >> >> r. >> >> >>> >> >>> >> >> >> >> >> And that is mainly the reason why VOTCA >> >> >>> >> >>> >> >> >> >> >> cannot >> >> >>> >> >>> >> >> >> >> >> handle >> >> >>> >> >>> >> >> >> >> >> it, >> >> >>> >> >>> >> >> >> >> >> ACI-ACI.dist.tgt is not a common rdf! >> >> >>> >> >>> >> >> >> >> >> You will have to provide an initial guess >> >> >>> >> >>> >> >> >> >> >> (pot.in) >> >> >>> >> >>> >> >> >> >> >> to >> >> >>> >> >>> >> >> >> >> >> make >> >> >>> >> >>> >> >> >> >> >> it >> >> >>> >> >>> >> >> >> >> >> work. >> >> >>> >> >>> >> >> >> >> >> (Please also read my email from July 10th >> >> >>> >> >>> >> >> >> >> >> again.) >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> Second, VOTCA does exactly what it is >> >> >>> >> >>> >> >> >> >> >> supposed >> >> >>> >> >>> >> >> >> >> >> to >> >> >>> >> >>> >> >> >> >> >> do. >> >> >>> >> >>> >> >> >> >> >> Go >> >> >>> >> >>> >> >> >> >> >> into >> >> >>> >> >>> >> >> >> >> >> gnuplot >> >> >>> >> >>> >> >> >> >> >> and >> >> >>> >> >>> >> >> >> >> >> run: >> >> >>> >> >>> >> >> >> >> >> p [0:3][-20:5] "ACI-ACI.dist.tgt" u >> >> >>> >> >>> >> >> >> >> >> 1:(-2.49435*log($2)-5.7) w >> >> >>> >> >>> >> >> >> >> >> l, >> >> >>> >> >>> >> >> >> >> >> "ACI-ACI.pot.cur" w l >> >> >>> >> >>> >> >> >> >> >> Except for some small deviations, which come >> >> >>> >> >>> >> >> >> >> >> from >> >> >>> >> >>> >> >> >> >> >> the >> >> >>> >> >>> >> >> >> >> >> cubic >> >> >>> >> >>> >> >> >> >> >> spline >> >> >>> >> >>> >> >> >> >> >> interpolation, there is no difference in the >> >> >>> >> >>> >> >> >> >> >> curves. >> >> >>> >> >>> >> >> >> >> >> As Victor said before, VOTCA shifts the >> >> >>> >> >>> >> >> >> >> >> potential >> >> >>> >> >>> >> >> >> >> >> to be >> >> >>> >> >>> >> >> >> >> >> zero >> >> >>> >> >>> >> >> >> >> >> at >> >> >>> >> >>> >> >> >> >> >> the >> >> >>> >> >>> >> >> >> >> >> cutoff -> -10.433 - 5.7 = -16.1. This shift >> >> >>> >> >>> >> >> >> >> >> of >> >> >>> >> >>> >> >> >> >> >> 5.7 >> >> >>> >> >>> >> >> >> >> >> makes >> >> >>> >> >>> >> >> >> >> >> no >> >> >>> >> >>> >> >> >> >> >> difference >> >> >>> >> >>> >> >> >> >> >> for the thermodynamics however. >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> Third, even pot.new is correct. Run >> >> >>> >> >>> >> >> >> >> >> $ paste ACI-ACI.dist.new <(sed '/^#/d' >> >> >>> >> >>> >> >> >> >> >> ACI-ACI.dist.tgt) >> >> >>> >> >>> >> >> >> >> >> <(sed >> >> >>> >> >>> >> >> >> >> >> '/^#/d' >> >> >>> >> >>> >> >> >> >> >> ACI-ACI.pot.cur) > ACI-ACI.temp >> >> >>> >> >>> >> >> >> >> >> to generate a temp file. >> >> >>> >> >>> >> >> >> >> >> And go into gnuplot and plot: >> >> >>> >> >>> >> >> >> >> >> p [0:3][-20:5] "ACI-ACI.temp" u >> >> >>> >> >>> >> >> >> >> >> 1:(2.49435*log($2/$5)+$8-16.1) >> >> >>> >> >>> >> >> >> >> >> w >> >> >>> >> >>> >> >> >> >> >> l, >> >> >>> >> >>> >> >> >> >> >> "ACI-ACI.pot.new" w l >> >> >>> >> >>> >> >> >> >> >> There is basically no difference in the >> >> >>> >> >>> >> >> >> >> >> curves. >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> Conclusion: >> >> >>> >> >>> >> >> >> >> >> - check your distributions again >> >> >>> >> >>> >> >> >> >> >> - provide pot.in for the interaction, which >> >> >>> >> >>> >> >> >> >> >> don't >> >> >>> >> >>> >> >> >> >> >> have >> >> >>> >> >>> >> >> >> >> >> a >> >> >>> >> >>> >> >> >> >> >> "common" >> >> >>> >> >>> >> >> >> >> >> rdf >> >> >>> >> >>> >> >> >> >> >> (meaning which doesn't go to 1) >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> Christoph >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> > W dniu poniedziałek, 15 lipca 2013 12:59:40 >> >> >>> >> >>> >> >> >> >> >> > UTC+1 >> >> >>> >> >>> >> >> >> >> >> > użytkownik >> >> >>> >> >>> >> >> >> >> >> > [email protected] napisał: >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> W dniu poniedziałek, 15 lipca 2013 >> >> >>> >> >>> >> >> >> >> >> >> 12:42:37 >> >> >>> >> >>> >> >> >> >> >> >> UTC+1 >> >> >>> >> >>> >> >> >> >> >> >> użytkownik >> >> >>> >> >>> >> >> >> >> >> >> Victor >> >> >>> >> >>> >> >> >> >> >> >> Rühle >> >> >>> >> >>> >> >> >> >> >> >> napisał: >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> Dear Steven, >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> provided the same kBT was used, I can >> >> >>> >> >>> >> >> >> >> >> >>> think >> >> >>> >> >>> >> >> >> >> >> >>> of >> >> >>> >> >>> >> >> >> >> >> >>> two >> >> >>> >> >>> >> >> >> >> >> >>> issues >> >> >>> >> >>> >> >> >> >> >> >>> which >> >> >>> >> >>> >> >> >> >> >> >>> might >> >> >>> >> >>> >> >> >> >> >> >>> lead to these differences >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> 1) votca can shift the potential, but the >> >> >>> >> >>> >> >> >> >> >> >>> shape >> >> >>> >> >>> >> >> >> >> >> >>> should >> >> >>> >> >>> >> >> >> >> >> >>> match. >> >> >>> >> >>> >> >> >> >> >> >>> That >> >> >>> >> >>> >> >> >> >> >> >>> can >> >> >>> >> >>> >> >> >> >> >> >>> in >> >> >>> >> >>> >> >> >> >> >> >>> particular happen if you cut the rdf in a >> >> >>> >> >>> >> >> >> >> >> >>> region >> >> >>> >> >>> >> >> >> >> >> >>> where >> >> >>> >> >>> >> >> >> >> >> >>> there >> >> >>> >> >>> >> >> >> >> >> >>> are >> >> >>> >> >>> >> >> >> >> >> >>> still >> >> >>> >> >>> >> >> >> >> >> >>> modulations. >> >> >>> >> >>> >> >> >> >> >> >>> 2) What type of potential are you lookin >> >> >>> >> >>> >> >> >> >> >> >>> at? >> >> >>> >> >>> >> >> >> >> >> >>> For >> >> >>> >> >>> >> >> >> >> >> >>> bonds >> >> >>> >> >>> >> >> >> >> >> >>> and >> >> >>> >> >>> >> >> >> >> >> >>> angles, >> >> >>> >> >>> >> >> >> >> >> >>> there >> >> >>> >> >>> >> >> >> >> >> >>> is indeed a normalization necessary, see >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> http://dx.doi.org/10.1002/(SICI)1521-4044(199802)49:2/3<61::AID-APOL61>3.0.CO;2-V >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> Thank you. I am looking at the nonbonded >> >> >>> >> >>> >> >> >> >> >> >> interactions >> >> >>> >> >>> >> >> >> >> >> >> only. >> >> >>> >> >>> >> >> >> >> >> >> The >> >> >>> >> >>> >> >> >> >> >> >> shape >> >> >>> >> >>> >> >> >> >> >> >> of >> >> >>> >> >>> >> >> >> >> >> >> the potential matches but the minima is >> >> >>> >> >>> >> >> >> >> >> >> lower >> >> >>> >> >>> >> >> >> >> >> >> than >> >> >>> >> >>> >> >> >> >> >> >> from >> >> >>> >> >>> >> >> >> >> >> >> my >> >> >>> >> >>> >> >> >> >> >> >> calulation. >> >> >>> >> >>> >> >> >> >> >> >> There >> >> >>> >> >>> >> >> >> >> >> >> is no normalization for non bonded so this >> >> >>> >> >>> >> >> >> >> >> >> is >> >> >>> >> >>> >> >> >> >> >> >> weird. >> >> >>> >> >>> >> >> >> >> >> >> I >> >> >>> >> >>> >> >> >> >> >> >> cut >> >> >>> >> >>> >> >> >> >> >> >> it >> >> >>> >> >>> >> >> >> >> >> >> at >> >> >>> >> >>> >> >> >> >> >> >> the >> >> >>> >> >>> >> >> >> >> >> >> begining as there were very small values >> >> >>> >> >>> >> >> >> >> >> >> and >> >> >>> >> >>> >> >> >> >> >> >> Votca >> >> >>> >> >>> >> >> >> >> >> >> was >> >> >>> >> >>> >> >> >> >> >> >> not >> >> >>> >> >>> >> >> >> >> >> >> able >> >> >>> >> >>> >> >> >> >> >> >> to >> >> >>> >> >>> >> >> >> >> >> >> extrapolate it properly. >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> Your second point indeed sounds a bit >> >> >>> >> >>> >> >> >> >> >> >>> weired. >> >> >>> >> >>> >> >> >> >> >> >>> Could >> >> >>> >> >>> >> >> >> >> >> >>> you >> >> >>> >> >>> >> >> >> >> >> >>> please >> >> >>> >> >>> >> >> >> >> >> >>> post >> >> >>> >> >>> >> >> >> >> >> >>> these >> >> >>> >> >>> >> >> >> >> >> >>> few curves to help debugging (i.e. the >> >> >>> >> >>> >> >> >> >> >> >>> <name>.pot.cur, >> >> >>> >> >>> >> >> >> >> >> >>> <name>.pot.new >> >> >>> >> >>> >> >> >> >> >> >>> <name>.dist.tgt <name>.dist.new of the >> >> >>> >> >>> >> >> >> >> >> >>> iteration 1 >> >> >>> >> >>> >> >> >> >> >> >>> folder)? >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> Victor >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> Please, see attached. >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> 2013/7/15 <[email protected]> >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> Dear Votca Users, >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> I have to issues with IBI: >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> 1) I took one my ditributions and >> >> >>> >> >>> >> >> >> >> >> >>>> calculated >> >> >>> >> >>> >> >> >> >> >> >>>> on my >> >> >>> >> >>> >> >> >> >> >> >>>> own >> >> >>> >> >>> >> >> >> >> >> >>>> potential >> >> >>> >> >>> >> >> >> >> >> >>>> W= >> >> >>> >> >>> >> >> >> >> >> >>>> -kBT >> >> >>> >> >>> >> >> >> >> >> >>>> ln(RDF) and I got different potential >> >> >>> >> >>> >> >> >> >> >> >>>> than >> >> >>> >> >>> >> >> >> >> >> >>>> Votca >> >> >>> >> >>> >> >> >> >> >> >>>> provide >> >> >>> >> >>> >> >> >> >> >> >>>> me. >> >> >>> >> >>> >> >> >> >> >> >>>> For >> >> >>> >> >>> >> >> >> >> >> >>>> instance >> >> >>> >> >>> >> >> >> >> >> >>>> lets calculate the potential minimum for >> >> >>> >> >>> >> >> >> >> >> >>>> the >> >> >>> >> >>> >> >> >> >> >> >>>> distribution >> >> >>> >> >>> >> >> >> >> >> >>>> maximum >> >> >>> >> >>> >> >> >> >> >> >>>> of >> >> >>> >> >>> >> >> >> >> >> >>>> 162. >> >> >>> >> >>> >> >> >> >> >> >>>> Pot = -.249435*ln(164) = -12.69. The >> >> >>> >> >>> >> >> >> >> >> >>>> minimum >> >> >>> >> >>> >> >> >> >> >> >>>> of >> >> >>> >> >>> >> >> >> >> >> >>>> Votca >> >> >>> >> >>> >> >> >> >> >> >>>> potential >> >> >>> >> >>> >> >> >> >> >> >>>> corresponds >> >> >>> >> >>> >> >> >> >> >> >>>> to approximately -16 kJ/mol. Where I >> >> >>> >> >>> >> >> >> >> >> >>>> missed >> >> >>> >> >>> >> >> >> >> >> >>>> something? is >> >> >>> >> >>> >> >> >> >> >> >>>> it >> >> >>> >> >>> >> >> >> >> >> >>>> somehow >> >> >>> >> >>> >> >> >> >> >> >>>> normalized? >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> 2) After 1st iteration my distribution >> >> >>> >> >>> >> >> >> >> >> >>>> was >> >> >>> >> >>> >> >> >> >> >> >>>> much >> >> >>> >> >>> >> >> >> >> >> >>>> higher >> >> >>> >> >>> >> >> >> >> >> >>>> than >> >> >>> >> >>> >> >> >> >> >> >>>> the >> >> >>> >> >>> >> >> >> >> >> >>>> target >> >> >>> >> >>> >> >> >> >> >> >>>> one so I guess the potential should >> >> >>> >> >>> >> >> >> >> >> >>>> decrease >> >> >>> >> >>> >> >> >> >> >> >>>> but >> >> >>> >> >>> >> >> >> >> >> >>>> apparently >> >> >>> >> >>> >> >> >> >> >> >>>> the >> >> >>> >> >>> >> >> >> >> >> >>>> new >> >> >>> >> >>> >> >> >> >> >> >>>> potential has deeper minima so the next >> >> >>> >> >>> >> >> >> >> >> >>>> distribution >> >> >>> >> >>> >> >> >> >> >> >>>> has >> >> >>> >> >>> >> >> >> >> >> >>>> a >> >> >>> >> >>> >> >> >> >> >> >>>> even >> >> >>> >> >>> >> >> >> >> >> >>>> higer >> >> >>> >> >>> >> >> >> >> >> >>>> distribution. Could anyone please >> >> >>> >> >>> >> >> >> >> >> >>>> explain >> >> >>> >> >>> >> >> >> >> >> >>>> me >> >> >>> >> >>> >> >> >> >> >> >>>> this? >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> Steven >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> -- >> >> >>> >> >>> >> >> >> >> >> >>>> You received this message because you >> >> >>> >> >>> >> >> >> >> >> >>>> are >> >> >>> >> >>> >> >> >> >> >> >>>> subscribed >> >> >>> >> >>> >> >> >> >> >> >>>> to >> >> >>> >> >>> >> >> >> >> >> >>>> the >> >> >>> >> >>> >> >> >> >> >> >>>> Google >> >> >>> >> >>> >> >> >> >> >> >>>> Groups "votca" group. >> >> >>> >> >>> >> >> >> >> >> >>>> To unsubscribe from this group and stop >> >> >>> >> >>> >> >> >> >> >> >>>> receiving >> >> >>> >> >>> >> >> >> >> >> >>>> emails >> >> >>> >> >>> >> >> >> >> >> >>>> from >> >> >>> >> >>> >> >> >> >> >> >>>> it, >> >> >>> >> >>> >> >> >> >> >> >>>> send >> >> >>> >> >>> >> >> >> >> >> >>>> an email to >> >> >>> >> >>> >> >> >> >> >> >>>> [email protected]. >> >> >>> >> >>> >> >> >> >> >> >>>> To post to this group, send email to >> >> >>> >> >>> >> >> >> >> >> >>>> [email protected]. >> >> >>> >> >>> >> >> >> >> >> >>>> Visit this group at >> >> >>> >> >>> >> >> >> >> >> >>>> http://groups.google.com/group/votca. >> >> >>> >> >>> >> >> >> >> >> >>>> For more options, visit >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> https://groups.google.com/groups/opt_out. >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> >>> >> >> >>> >> >>> >> >> >> >> >> > -- >> >> >>> >> >>> >> >> >> >> >> > You received this message because you are >> >> >>> >> >>> >> >> >> >> >> > subscribed >> >> >>> >> >>> >> >> >> >> >> > to >> >> >>> >> >>> >> >> >> >> >> > the >> >> >>> >> >>> >> >> >> >> >> > Google >> >> >>> >> >>> >> >> >> >> >> > Groups >> >> >>> >> >>> >> >> >> >> >> > "votca" group. >> >> >>> >> >>> >> >> >> >> >> > To unsubscribe from this group and stop >> >> >>> >> >>> >> >> >> >> >> > receiving >> >> >>> >> >>> >> >> >> >> >> > emails >> >> >>> >> >>> >> >> >> >> >> > from >> >> >>> >> >>> >> >> >> >> >> > it, >> >> >>> >> >>> >> >> >> >> >> > send >> >> >>> >> >>> >> >> >> >> >> > an >> >> >>> >> >>> >> >> >> >> >> > email to [email protected]. >> >> >>> >> >>> >> >> >> >> >> > To post to this group, send email to >> >> >>> >> >>> >> >> >> >> >> > [email protected]. >> >> >>> >> >>> >> >> >> >> >> > Visit this group at >> >> >>> >> >>> >> >> >> >> >> > http://groups.google.com/group/votca. >> >> >>> >> >>> >> >> >> >> >> > For more options, visit >> >> >>> >> >>> >> >> >> >> >> > https://groups.google.com/groups/opt_out. >> >> >>> >> >>> >> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >> >> >>> >> >>> >> >> >> >> >> -- >> >> >>> >> >>> >> >> >> >> >> Christoph Junghans >> >> >>> >> >>> >> >> >> >> >> Web: http://www.compphys.de >> >> >>> >> >>> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> > -- >> >> >>> >> >>> >> >> >> >> > You received this message because you are >> >> >>> >> >>> >> >> >> >> > subscribed >> >> >>> >> >>> >> >> >> >> > to >> >> >>> >> >>> >> >> >> >> > the >> >> >>> >> >>> >> >> >> >> > Google >> >> >>> >> >>> >> >> >> >> > Groups >> >> >>> >> >>> >> >> >> >> > "votca" group. >> >> >>> >> >>> >> >> >> >> > To unsubscribe from this group and stop >> >> >>> >> >>> >> >> >> >> > receiving >> >> >>> >> >>> >> >> >> >> > emails >> >> >>> >> >>> >> >> >> >> > from >> >> >>> >> >>> >> >> >> >> > it, >> >> >>> >> >>> >> >> >> >> > send >> >> >>> >> >>> >> >> >> >> > an >> >> >>> >> >>> >> >> >> >> > email to [email protected]. >> >> >>> >> >>> >> >> >> >> > To post to this group, send email to >> >> >>> >> >>> >> >> >> >> > [email protected]. >> >> >>> >> >>> >> >> >> >> > Visit this group at >> >> >>> >> >>> >> >> >> >> > http://groups.google.com/group/votca. >> >> >>> >> >>> >> >> >> >> > For more options, visit >> >> >>> >> >>> >> >> >> >> > https://groups.google.com/groups/opt_out. >> >> >>> >> >>> >> >> >> >> > >> >> >>> >> >>> >> >> >> >> > >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > -- >> >> >>> >> >>> >> >> >> > You received this message because you are >> >> >>> >> >>> >> >> >> > subscribed >> >> >>> >> >>> >> >> >> > to >> >> >>> >> >>> >> >> >> > the >> >> >>> >> >>> >> >> >> > Google >> >> >>> >> >>> >> >> >> > Groups >> >> >>> >> >>> >> >> >> > "votca" group. >> >> >>> >> >>> >> >> >> > To unsubscribe from this group and stop receiving >> >> >>> >> >>> >> >> >> > emails >> >> >>> >> >>> >> >> >> > from >> >> >>> >> >>> >> >> >> > it, >> >> >>> >> >>> >> >> >> > send >> >> >>> >> >>> >> >> >> > an >> >> >>> >> >>> >> >> >> > email to [email protected]. >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > To post to this group, send email to >> >> >>> >> >>> >> >> >> > [email protected]. >> >> >>> >> >>> >> >> >> > Visit this group at >> >> >>> >> >>> >> >> >> > http://groups.google.com/group/votca. >> >> >>> >> >>> >> >> >> > For more options, visit >> >> >>> >> >>> >> >> >> > https://groups.google.com/groups/opt_out. >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> > >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> >> >> >>> >> >>> >> >> >> -- >> >> >>> >> >>> >> >> >> Christoph Junghans >> >> >>> >> >>> >> >> >> Web: http://www.compphys.de >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> > -- >> >> >>> >> >>> >> >> > You received this message because you are subscribed >> >> >>> >> >>> >> >> > to >> >> >>> >> >>> >> >> > the >> >> >>> >> >>> >> >> > Google >> >> >>> >> >>> >> >> > Groups >> >> >>> >> >>> >> >> > "votca" group. >> >> >>> >> >>> >> >> > To unsubscribe from this group and stop receiving >> >> >>> >> >>> >> >> > emails >> >> >>> >> >>> >> >> > from >> >> >>> >> >>> >> >> > it, >> >> >>> >> >>> >> >> > send >> >> >>> >> >>> >> >> > an >> >> >>> >> >>> >> >> > email to [email protected]. >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> > To post to this group, send email to >> >> >>> >> >>> >> >> > [email protected]. >> >> >>> >> >>> >> >> > Visit this group at >> >> >>> >> >>> >> >> > http://groups.google.com/group/votca. >> >> >>> >> >>> >> >> > For more options, visit >> >> >>> >> >>> >> >> > https://groups.google.com/groups/opt_out. >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> > >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> >> >> >>> >> >>> >> >> -- >> >> >>> >> >>> >> >> Christoph Junghans >> >> >>> >> >>> >> >> Web: http://www.compphys.de >> >> >>> >> >>> >> > >> >> >>> >> >>> >> > -- >> >> >>> >> >>> >> > You received this message because you are subscribed to >> >> >>> >> >>> >> > the >> >> >>> >> >>> >> > Google >> >> >>> >> >>> >> > Groups >> >> >>> >> >>> >> > "votca" group. >> >> >>> >> >>> >> > To unsubscribe from this group and stop receiving >> >> >>> >> >>> >> > emails >> >> >>> >> >>> >> > from >> >> >>> >> >>> >> > it, >> >> >>> >> >>> >> > send >> >> >>> >> >>> >> > an >> >> >>> >> >>> >> > email to [email protected]. >> >> >>> >> >>> >> > To post to this group, send email to >> >> >>> >> >>> >> > [email protected]. >> >> >>> >> >>> >> > Visit this group at >> >> >>> >> >>> >> > http://groups.google.com/group/votca. >> >> >>> >> >>> >> > For more options, visit >> >> >>> >> >>> >> > https://groups.google.com/groups/opt_out. >> >> >>> >> >>> >> > >> >> >>> >> >>> >> > >> >> >>> >> >>> >> >> >> >>> >> >>> >> >> >> >>> >> >>> >> >> >> >>> >> >>> >> -- >> >> >>> >> >>> >> Christoph Junghans >> >> >>> >> >>> >> Web: http://www.compphys.de >> >> >>> >> >>> > >> >> >>> >> >>> > -- >> >> >>> >> >>> > You received this message because you are subscribed to >> >> >>> >> >>> > the >> >> >>> >> >>> > Google >> >> >>> >> >>> > Groups >> >> >>> >> >>> > "votca" group. >> >> >>> >> >>> > To unsubscribe from this group and stop receiving emails >> >> >>> >> >>> > from >> >> >>> >> >>> > it, >> >> >>> >> >>> > send >> >> >>> >> >>> > an >> >> >>> >> >>> > email to [email protected]. >> >> >>> >> >>> > To post to this group, send email to >> >> >>> >> >>> > [email protected]. >> >> >>> >> >>> > Visit this group at http://groups.google.com/group/votca. >> >> >>> >> >>> > For more options, visit >> >> >>> >> >>> > https://groups.google.com/groups/opt_out. >> >> >>> >> >>> > >> >> >>> >> >>> > >> >> >>> >> >>> >> >> >>> >> >>> >> >> >>> >> >>> >> >> >>> >> >>> -- >> >> >>> >> >>> Christoph Junghans >> >> >>> >> >>> Web: http://www.compphys.de >> >> >>> >> > >> >> >>> >> > -- >> >> >>> >> > You received this message because you are subscribed to the >> >> >>> >> > Google >> >> >>> >> > Groups >> >> >>> >> > "votca" group. >> >> >>> >> > To unsubscribe from this group and stop receiving emails from >> >> >>> >> > it, >> >> >>> >> > send >> >> >>> >> > an >> >> >>> >> > email to [email protected]. >> >> >>> >> > To post to this group, send email to [email protected]. >> >> >>> >> > Visit this group at http://groups.google.com/group/votca. >> >> >>> >> > For more options, visit >> >> >>> >> > https://groups.google.com/groups/opt_out. >> >> >>> >> > >> >> >>> >> > >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> -- >> >> >>> >> Christoph Junghans >> >> >>> >> Web: http://www.compphys.de >> >> >>> > >> >> >>> > -- >> >> >>> > You received this message because you are subscribed to the >> >> >>> > Google >> >> >>> > Groups >> >> >>> > "votca" group. >> >> >>> > To unsubscribe from this group and stop receiving emails from it, >> >> >>> > send >> >> >>> > an >> >> >>> > email to [email protected]. >> >> >>> > To post to this group, send email to [email protected]. >> >> >>> > Visit this group at http://groups.google.com/group/votca. >> >> >>> > For more options, visit https://groups.google.com/groups/opt_out. >> >> >>> > >> >> >>> > >> >> >>> >> >> >>> >> >> >>> >> >> >>> -- >> >> >>> Christoph Junghans >> >> >>> Web: http://www.compphys.de >> >> > >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> >> > send >> >> > an >> >> > email to [email protected]. >> >> > To post to this group, send email to [email protected]. >> >> > Visit this group at http://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> > >> >> > >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
