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:
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?
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
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