W dniu wtorek, 13 sierpnia 2013 17:37:21 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/8/13 <[email protected] <javascript:>>: > > > > > > 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 >
My atomistic simulation was run at NPT ensemble with a cubic box dimension of 95A with fully explicit solvent. Now I do not have water as I want to include it in the non bonded parameters.Previously I had a box of 150A in IBI (NVT - no water) and distributions looked like I attached in my 1st post - Same shape but much higher (the box is bigger the bigger the distributions). Now I set up the box to 95A in and running IBI in NVT and they have similar shape and values- they are converging. Is that a good approach? Or shall I use nopbc option in mdp as you suggested and try to converge it to atomisitic distributions without pbc as well? Steven > >> > > >> > > >> > 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] <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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