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] <javascript:>>: > > 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] <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. > > > > > > > > -- > 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.
