I used different software ACEMD driving my protein from 300K to 500K thousands of times to explore or possible conformations...so the box dimension was changing from 9.4 to 11.4 nm. At 300K it had 9.4 nm. I used all the states corresponding to 300K only. No I will change the box in my CG iterative method to 9.4 nm as I had 12 nm no clue why... Should work fine now. Thank you!
W dniu wtorek, 13 sierpnia 2013 11:08:21 UTC+1 użytkownik Valentina Erastova napisał: > > 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] <javascript:> 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] <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.
