Hi Sebastian, The problem is solved. The the molecular name matters. Thanks a lot!
Best, Han On Wednesday, January 30, 2013 1:25:02 PM UTC+1, Sebastian wrote: > > On 01/30/2013 12:03 PM, Han Wang wrote: > > Hi Han, > > > I dont know if it helps, but you may try too look at your topology with > csg_dump to see how votca reads the molecule names. Btw.: you can also > use wildcards (--molname Meth*) to extend your selection to all > molecules beginin with Meth. > > Best > Sebastian > > Hi, > > > > I am calculating the thermodynamic force for the methane solved in > > water system. The scg_density program complains the following > > > > Running critical command 'csg_density --trj traj.xtc --top topol.tpr > > --out Meth.dist.new --begin 10 --first-frame 0 --molname Meth --axis x > > --step 0.01' > > Reading file topol.tpr, VERSION 4.6.1-dev-20130124-fb5b9bd-dirty > > (single precision) > > I have 13756 beads in 3456 molecules > > Reading frame 0 time 0.000 > > Reading frame 10 time 10.000 rmax: 7.53057 > > axis: x > > Bins: 753 > > an error occurred: > > No molecule in selection > > > > why it complains "No molecule in selection" ? Although the density of > > methane is very low, it is possible in one frame one cannot find any > > molecule in one bin. But after doing average of a lot of frames, the > > density value is not zero for all bins, so the th force can be > > calculated. Can anybody suggest how to solve it? Thanks! > > > > Best, > > Han > > -- > > 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?hl=en. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > > -- > > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > -- 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.
