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] <javascript:>> > >> 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
ACI-ACI.dist.new
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ACI-ACI.dist.tgt
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ACI-ACI.pot.cur
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ACI-ACI.pot.new
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