2013/3/7 永乐李 <[email protected]>: > Sorry, the dist.xml file and MD file are here: > > https://www.dropbox.com/s/sbg8sxausjo5ryb/dist.xml > > https://www.dropbox.com/s/13geoo5nv3k0aew/test2.mdp > > > On Thursday, March 7, 2013 2:44:01 PM UTC-7, 永乐李 wrote: >> >> Hi all, >> >> Now I've finished two tutorials, spce and hexane. >> And I'm trying to do a simple test: >> >> I construct a small box containing 24 DOPE lipids, and did MD using >> Gromacs. >> >> Firstly, I used csg_dump to check the CG mapping: >> >> csg_dump --top testmd2.tpr --cg dope.xml >> Reading file testmd2.tpr, VERSION 4.5.5 (single precision) >> I have 3096 beads in 24 molecules >> I have 336 beads in 24 molecules for the coarsegraining >> >> List of molecules: >> molecule: 1 DOPE beads: 14 >> 0 NH3 Qd >> 1 PO4 Qa >> ... >> molecule: 2 DOPE beads: 14 >> ... >> 334 C4B C1 >> 335 C5B C1b >> f >> Everything seems OK. But when I use csg_stat to calculate distribution >> functions, it fails, leaving these error info: >> >> csg_stat --top testmd2.tpr --cg dope.xml --options dist.xml --trj >> testmd2.trr --begin 0 --first-frame 0 --nframes 10 >> begin to calculate distribution functions >> # of bonded interactions: 0 You can also calculate bonded distributions by adding bond/angle definition to the mapping file (see the hexane.xml mapping file) >> # of non-bonded interactions: 10 >> an error occurred: >> property not found: step >> >> Would you please help me to handle this problem? Thanks! Well, the interaction Nab-Qa has no step item.
>> >> P. S. >> And I also attach the dist.xml file and the MD input file. > > -- > 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?hl=en. > 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
