Sorry, my cell dimension was 95A (I was running temperature annealing so the box dimension changed). Where in tpr file can I see the actual cell dimension? I mean from where csg_stat takes the cell dimension to calculate RDFs?
Steven W dniu wtorek, 13 sierpnia 2013 10:49:13 UTC+1 użytkownik Valentina Erastova napisał: > > 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] <javascript:>> > 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] <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.
