Dear Votca Users,
I have a question about creating initial configuration of the system.
1. Full atomistic simulation ---- I have run full atomistic simulations
of polymer system with OPLS-AA force field. Then, it (low density system)
was equilibrated with NVT and NPT simulation for 50 ns. Thus, the box under
PBC is shrinked from 10nm to about 5nm.
2. Then, I used the final configuration (confout.gro) in order to map
the atomistic system into Coarse-grained system.
I used this CG system for IBI in order to get non-bonded potentials.
However, when I run IBI, I think that some of angle are blowing up and the
ibi run finally fail in the beginning. I checked CG trajectory. An angle
seem to be blowing up as shown in figure.
I think this is ok if the system is under PBC. But the error message
keeps indicate this angle has a problem.
Therefore, I am asking for how you create the initial CG system all
beads are inside box but not at the boundary.
Thank you.
****************************************************************************************************
Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
Tab. Angles of 856 missing 1
Molecule type 'TDM'
the first 10 missing interactions, except for exclusions:
Tab. Angles atoms 1 3 2 global 201 203 202
******************************************************************************************************
Best regards,
Changwoon Jang,
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