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]. > 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. > > > -- > 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.
