W dniu wtorek, 16 lipca 2013 08:48:51 UTC+1 użytkownik Tristan Bereau napisał: > > That sounds like what I was hinting at: from what I understand, you're > simulating a single protein, not a pure liquid of stuff. So your RDF > will never go to 1 because there won't be anything at large distances. > Is that the case? If so, more iterations and/or better initial guesses > won't cut it. >
Yes, this is the case. I will aproximate the RDFs so that they go to sth which is non zero. Thank you. Steven > > On Mon, Jul 15, 2013 at 10:09 PM, <[email protected] <javascript:>> > wrote: > > 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]>: > >> > 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] <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. 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