W dniu wtorek, 13 sierpnia 2013 14:54:16 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/8/13 <[email protected] <javascript:>>: > > 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. 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] <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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