Am 12.10.2015 12:43 vorm. schrieb "frank Zack" <[email protected]>: > > Thx for your reply. > Actually, the tuples and triples defined within the cg_bonded block for bonds and angles are correct. Its a simple topology, so i think that should not be the problem (In my new configuration and topology I only have a single bead 'SC1' representing a propene unit of poplypropylene). I guess something simple is wrong here! Can you share the two XML (mapping and settings) files with us?
> > Im using gromacs 5.0.7-dev-20151003-1909f2f-dirty, maybe that could be the problem? I don't think the gromacs version matters! > > Btw: Where is the benefit from using cg_stat for the computation of the distributions? Why not use gmx distace and gmx angle? csg_stat does all distributions at once and follows its own exclusion scheme! > Indeed gmx angle gave me a proper angle-distribution for my trajectory. Maybe I should try to replace the cg_stat analysis by gmx-tools? You think its worth a try, is it possible at all? Votca doesn't care where the target distributions come from, as long as the format is correct, so it depends if it is a single shot analysis or if it is ibi, where the distributions need to be calculated in each iteration step! > > regards, > frank. > > > Am Sonntag, 11. Oktober 2015 19:42:47 UTC+2 schrieb frank Zack: >> >> Hi, >> >> i created a coarse grained representation of a large polymer (appended) by biased mc. I dont have an atomistic representation of that system. So i created a "pseudo"-topo file and a "pseudo"-mapping file. >> I applied the hexane/ibi_bonded example to my system, but I guess I made some mistake in the mapping file (why do i need this it all for csg_stat?) because csg_stat doesnt find any angles. >> >> Pls see the attached files. Is there any obvious mistake? The trajectory file is too large (46 MB) for uploading here. You can get it here: >> https://www.dropbox.com/s/lmzir99zkth5srt/traj.xtc?dl=0 >> >> this is how i use csg_stat: >> >> ~/votca/bin/csg_stat --options ./settings.xml --top step_001/topol.tpr --trj step_001/traj.xtc --cg hexane_cg.xml --begin 10 >> >> no errors occur. but angle-dist is empty. >> >> thx for any advice, >> >> regards,frank > > -- > 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/d/optout. -- 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/d/optout.
