hi all :
I prepared top and rtp file for graphite using a command:
g_x2top -f input.gro -r output -o output in GMX (V 4.5.5).
A obvious mistake itp file is posted as below:
[ bonds ]
C1 C3776 1.420e-01 4.000e+05
C5 C3780 1.420e-01 4.000e+05
#####
for example，the distance between C1 and C3776 is at least 10 nm.
the coordination is below:
1GRA C1 1 0.000 0.000 0.000
1GRA C3776 3776 0.000 10.068 0.000
Thanks in advance for any suggestion.
sincrely，
zhhxu PhD student
Institute of Process Engineering, Chinese Academy of Sciences
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