W dniu wtorek, 13 sierpnia 2013 16:08:49 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/8/13 <[email protected] <javascript:>>: > > > > > > 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. other would be to use g_rdf script you provided me, yep? 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] <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. > > > > > > > > -- > 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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