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
> > 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.
