2013/12/27 Konstantin Koschke <[email protected]>: > Dear all, > > I've been using Espresso++ for my simulations, saving the trajectory > to a .gro file. > > I would like to use csg_stat to compute the radial distribution > function, but do not know how to specify the different types of atoms > for which the rdf should be computed. > > Sample (single frame) .gro file: > > system description, current step=1, length unit=LJ > 1872 > 1T0 T0 1 0.284 7.798 0.208 0.1758 -0.0315 -1.8179 > 2T0 T0 2 0.759 11.851 2.541 -0.3331 0.5601 -0.1017 > 3T0 T0 3 4.468 3.993 9.966 -2.0515 -0.5443 0.5865 > 4T0 T0 4 1.191 8.928 7.218 0.6759 -0.1850 0.7744 > 5T0 T0 5 2.372 1.933 11.360 0.3106 -0.1728 -2.0392 > 6T0 T0 6 8.341 1.811 10.498 0.2489 0.3545 1.7114 > 7T0 T0 7 7.774 11.684 11.541 0.9694 -1.0832 -1.7319 > 8T0 T0 8 6.976 5.328 0.700 -1.9203 -2.2488 0.1209 > 9T0 T0 9 9.434 6.609 5.760 -0.0652 1.8154 0.5061 > <snip> > 1864T1 T1 1864 9.047 0.116 5.381 0.5089 -1.8502 1.9424 > 1865T1 T1 1865 6.681 0.467 9.574 -2.1365 -0.1400 0.1403 > 1866T1 T1 1866 4.985 6.904 10.216 2.5356 -2.8845 -0.6594 > 1867T1 T1 1867 2.153 8.618 9.314 -2.1215 -1.8006 -0.8942 > 1868T1 T1 1868 0.297 0.925 2.052 -1.7950 -1.6092 0.3049 > 1869T1 T1 1869 1.739 5.657 10.281 0.6179 -1.4787 2.2130 > 1870T1 T1 1870 5.681 12.372 2.197 -2.1709 0.0992 2.2873 > 1871T1 T1 1871 2.140 2.912 8.940 -0.2329 -0.4645 -3.2850 > 1872T1 T1 1872 2.026 9.238 1.335 -0.0400 -0.0488 0.5568 > > relevant part of settings.xml: > <!-- types involved in this interaction --> > <type1>*</type1> > <type2>*</type2> > > $ csg_dump --top traj.gro > WARNING: topology created from .gro file, masses and charges are wrong! > I have 1872 beads in 0 molecules > > List of molecules: gro files contain no molecular information, you will need to create an xml topology based on your gro file. (see topol.xml in csg-tutorials/spce/ibi_espressopp as an example).
> csg_dump does not find the two types of atoms (T0, T1) and I don't > know what to put into the 'type' tags in the settings.xml. I would > like to compute the rdf between T0 and T1. Any suggestions? Once molecules are setup csg_dump will show you the types it found: $ csg_dump --top topol.xml ... molecule: 2180 SOL beads: 1 2179 Name 1:SOL:CG Type CG Mass 1 These types can be used in your settings.xml. Cheers, Christoph > > > Thank you! > konstantin > > PS. If necessary, I'll code. > > Konstantin Koschke > Schneckestr. 13 > 81737 München > > cell: +49 174 318 00 22 > landline: +49 89 8092 8193 > skype: der.konsi > > -- > 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. -- 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. For more options, visit https://groups.google.com/groups/opt_out.
