2013/8/13 <[email protected]>: > > > W dniu wtorek, 13 sierpnia 2013 16:08:49 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 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 > > > Thank you. I guess grompp will complain about no box dimension but it can be > done I guess with maxwarining option. Or you could make the box huge like I suggested earlier. Also gromacs has an mdp option pbc=no.
Anyhow, this is more a gromacs question, please post it on their mailing list. > other would be to use g_rdf script you provided me, yep? Maybe, but we removed that rdf script for several reasons, so there is no official support for it. If it doesn't work don't blame us ;-) Christoph > > Steven >> >> > >> > 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. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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