2015-11-12 19:15 GMT-07:00 <[email protected]>: > > Hello, Christoph > > In the appendix of the reference *Rühle V, Junghans C, Lukyanov A, et > al. Versatile object-oriented toolkit for coarse-graining applications[J]. > Journal of Chemical Theory and Computation, 2009, 5(12): 3211-3223.* > It requires that all interactions should be inputted by "fmatch.xml" > theoretically. > > > <https://lh3.googleusercontent.com/-ewba7Sf00LU/VkVENx2UvGI/AAAAAAAAAAc/mhClv_Xx9Hc/s1600/%25E6%258D%2595%25E8%258E%25B7.JPG> > Actually, I just put only one interaction in "fmatch.xml" as input, then > VOTCA output a normal result, whether it is correct or not. > Does it influence the result, when I input only one interaction? > If I remember the algorithm correctly, the difference between one vs. all at once is that, in the former case the least square is minimize for a single interaction not considering the others, while in the latter it is minimized for all at once. This might lead to different solutions.
Christoph > Thanks a lot ! > > Nickya > > > > 在 2015年11月11日星期三 UTC+8上午5:48:06，Christoph Junghans写道： >> >> 2015-11-09 19:21 GMT-07:00 <[email protected]>: >> > Hello, Rom, Christoph, Sikandar >> > >> > It seems that I got into the same trouble with you. >> > It was out of memory by using a large xml file. >> > Then I ran a single interaction or several interactions. >> > "Single" was much faster than "several". >> > However, some of the results were normol, some were "nan". >> > >> > ***.force >> > ... >> > 1.91 -2.89326427 3.107846992 i >> > 1.92 -1.848309842 2.648399863 i >> > 1.93 -0.5889638119 2.629085293 i >> > 1.94 0.4264542843 3.10001575 i >> > 1.95 0.7396249096 3.516476759 i >> > 1.96 0.06407534287 3.515091163 i >> > 1.97 -1.53992564 3.334205836 i >> > 1.98 -3.840262448 3.585295232 i >> > 1.99 -6.604819488 4.667911077 i >> > 2 -9.601481171 6.365280589 i >> > ... >> > >> > >> > ***.force >> > .. >> > 1.91 nan nan i >> > 1.92 nan nan i >> > 1.93 nan nan i >> > 1.94 nan nan i >> > 1.95 nan nan i >> > 1.96 nan nan i >> > 1.97 nan nan i >> > 1.98 nan nan i >> > 1.99 nan nan i >> > 2 nan nan i >> > ... >> > >> > >> > How to avoid these mistakes? >> You get NaNs if there is not enough statistics in each bin. Did you >> play with the frames_per_block option? >> The other option is to look at the rdf and pick min and max a little >> tighter, meaning so that it only covers the region where there is >> actually structure. >> >> Maybe the other Christoph can say something about that issue. >> >> Christoph >> >> >> > >> > Thanks in Advance, >> > Nickya >> > >> > -- >> > 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/d/optout. >> >> >> >> -- >> 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/d/optout. > -- 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/d/optout.
