So, you started with cubic box of 95A * 3 (gromacs units are nm)? Then you T annealed, got output confout.gro (with box size at the bottom of the file), change of the box size can be taken from trajectory.
I am not too sure about your method, tbh, as annealing is a funny thing - it can cause system to lag behind. Personally, I wouldn't use a system that potentially can not have reached equilibrium to get reference potentials for CG. .tpr is binary, i.e. you cannot read it. csg_stat - I am not sure, better ask developers, but I would expect it to come from the trajectory. V On 13 Aug 2013, at 10:56, [email protected] wrote: > 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]> > 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. > > -- 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.
