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.
