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 > > 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. 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