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....
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.
