By the way, i just checked the energy-file of the md-run and it seems like
bonds and angles are present:
time: 5.00000e+00 step: 5000
nsteps: 2500
delta_t: 1.00000e-03 sum steps: 25
Component Energy Av. Energy Sum Energy
Bond 2.31183e+04 9.89668e+08 7.47935e+05
Angle 1.28529e+04 1.90669e+08 4.03331e+05
LJ (SR) 0.00000e+00 0.00000e+00 0.00000e+00
Coulomb (SR) 0.00000e+00 0.00000e+00 0.00000e+00
Potential 3.59712e+04 2.04689e+09 1.15127e+06
Kinetic En. 4.10349e+04 1.81630e+09 1.27300e+06
Total Energy 7.70062e+04 7.71056e+09 2.42427e+06
Temperature 3.22603e+02 1.12258e+05 1.00079e+04
Pressure -1.22993e+02 1.61483e+04 -3.69099e+03
Vir-XX 1.73216e+04 3.46148e+08 5.47452e+05
Vir-XY 1.34344e+02 4.79610e+06 3.67023e+03
However, nor a bond-distribution nor an angle-distribution is produced by
cg_stat
whats groing wrong?
Am Sonntag, 11. Oktober 2015 19:42:47 UTC+2 schrieb frank Zack:
>
> Hi,
>
> i created a coarse grained representation of a large polymer (appended) by
> biased mc. I dont have an atomistic representation of that system. So i
> created a "pseudo"-topo file and a "pseudo"-mapping file.
> I applied the hexane/ibi_bonded example to my system, but I guess I made
> some mistake in the mapping file (why do i need this it all for csg_stat?)
> because csg_stat doesnt find any angles.
>
> Pls see the attached files. Is there any obvious mistake? The trajectory
> file is too large (46 MB) for uploading here. You can get it here:
> https://www.dropbox.com/s/lmzir99zkth5srt/traj.xtc?dl=0
>
> this is how i use csg_stat:
>
> ~/votca/bin/csg_stat --options ./settings.xml --top step_001/topol.tpr
> --trj step_001/traj.xtc --cg hexane_cg.xml --begin 10
>
> no errors occur. but angle-dist is empty.
>
> thx for any advice,
>
> regards,frank
>
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