Or is there any command which will tell csg_stat to get rid of PBC so that cell dimension will not have influcence on RDFs? I mean target distributions as well as during the iterations in IBI?
Steven W dniu wtorek, 13 sierpnia 2013 11:34:51 UTC+1 użytkownik Valentina Erastova napisał: > > > On 13 Aug 2013, at 11:27, [email protected] <javascript:> wrote: > > > > W dniu wtorek, 13 sierpnia 2013 11:24:59 UTC+1 użytkownik Valentina > Erastova napisał: >> >> >> On 13 Aug 2013, at 11:21, [email protected] wrote: >> >> 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! >> >> >> May be some inconsistence with trajectory reading. >> Never used AceMD. >> V >> >> > You better try that :) 60 ns a day with 100 K atoms using temp annealing > ar one GPU :) > > > Just implemented material science FFs onto gromacs, not reimplementing > again (pain). But sounds good;) > > > >> 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] 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. >> >> >> >> >> > -- > 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.
