Hi, I am a little confused there.
You need to have a well equilibrated system before you CG. My way is to run NPT, but make sure that the system is equilibrated and V is also constant. When you start CG, I would use NVT, check what is the P (normally completely off), then do a P-correction. Good luck, V On 13 Aug 2013, at 10:37, <[email protected]> wrote: > I think I know where is the reason... I set the wrong unit cell in my CG > model. However, I run full atomistic in NPT and the cubic unit cell was > changing between 94A and 114A. Which shall I set up in my CG run then which > is in NVT? > > W dniu poniedziałek, 12 sierpnia 2013 17:02:36 UTC+1 użytkownik Valentina > Erastova napisał: > Hi, have you used scaling by by 1 /4 \pi r^2for bond and by 1/ sin (\theta) > for angle distribution? > > I assume those are angles & bonds. > > Best, > V > > > > On 12 Aug 2013, at 16:39, [email protected] wrote: > >> Dear Users, >> >> I run 7500 iterations of the protein with 5 different bead types so 15 >> distributions. Please, see attached 4 examples - black atomistic, red >> coarse-grained. >> 14 of them have exactly the same shapes as atomistic but have higher values >> and they stopped converging after 6000 steps. Only one (attached) perfectly >> converged. >> May that be the reason of the one converged so its a wrong distribution so >> the other cannot? Or everything is ok and I just to normalize them? >> >> Thank you, >> >> 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. >> >> >> <Dsitributions_RDF.png> > > > -- > 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.
