2013/7/15 <[email protected]>: > > > W dniu poniedziałek, 15 lipca 2013 21:09:27 UTC+1 użytkownik > [email protected] napisał: >> >> 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 > > > And to be clear: My potentials goes o zero at large r. What do you mean?
> > 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. > > -- 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.
