csg_stat must read the cell dimension from tpr files - you can see what is inside with gmxdupm -s topol.tpr | more. So if I change in my conf.gro the cell dimension it will prodcue tpr files with grommp corresponding to a proper cell so that distributions will match. When increasing the box diemnsions the RDFs have higher values. Can developer confirm that csg_stat takes the cell dimension for inderirectly RDFs from either conf.gro ?
Steven W dniu wtorek, 13 sierpnia 2013 11:21:04 UTC+1 użytkownik [email protected] napisał: > > 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! > > 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.
