2013/8/13 <[email protected]>: > > > W dniu wtorek, 13 sierpnia 2013 14:54:16 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 2013/8/13 <[email protected]>: >> > 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? >> VOTCA reads the box from the tpr file. One could use a gro file as a >> topology (--top conf.gro), but the gro file contains less information >> (e.g. charges, mass, types will be wrong.). Gro files contain a box, >> too, but for some reason, which I don't remember right now, VOTCA >> won't use it. >> >> You can use a different topology file to calculate the rdfs >> (cg.inverse.gromacs.topol). We originally added this feature, so that >> one can calculated rdfs with a different number of exclusions, but one >> can also use that to use a different box. In your case just make the >> box huge. >> >> Cheers, >> >> Christoph > > > Thank you. But when I set up the conf.gro to the box average from atomistic > simulations the tpr file by grompp will be set up correctly. I tried this > and all profiles are converging. However, the more accurate will be RDF > which does not account the box size so without pbc. Is there any command in > csg_stat which can calculate this like g_rdf -nopbc option? I realised in > VMD that when changing the cell dimension RDFs changes....which makes sense. > When setup without box size (dont use pbc) I got normalized distributions > which will be more accurate in my case. No, csg_stat doesn't have such an option! (see "csg_stat --help" for details). However, feel free to add one ;-)
Like I said before, the easiest in your case will be to create a special tpr with no box beforehand and give it to csg_stat via the cg.inverse.gromacs.topol option, so that the special tpr is only used for the rdf calculation, but not for the simulation. Christoph > > Steven > >> >> > >> > 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] 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]. >> >> 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. >> > >> > >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > 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. > > -- Christoph Junghans Web: http://www.compphys.de -- 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.
