2013/7/25 <[email protected]>: > > > On Thursday, July 25, 2013 1:33:10 PM UTC+1, [email protected] wrote: >> >> >> >> 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" - done >>> - add that directory to cg.inverse.scriptdir in your xml file - done >>> >>> - create a file csg_table with the following line >>> rdf gromacs my_rdf.sh - in the main directory or in scripts folder? >>> >>> - get the default rdf calculation script: >>> $ csg_call --show rdf gromacs >>> - same it under the name my_rdf.sh >>> - modify my_rdf.sh >> >> > Dont understand last three "-" : $ csg_call --show rdf gromacsis inside > my_rdf.sh ? where would I shouldplace my g_rdf command? $ csg_call --show rdf gromacs /home/junghans/votca/share/votca/scripts/inverse/calc_rdf_generic.sh now save it under my_rdf.sh cp /home/junghans/votca/share/votca/scripts/inverse/calc_rdf_generic.sh my_rdf.sh Modify it.
> > Sorry for silly questions, > > Steven >> >> >> 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> >> >> ??? >> >> 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.
