Dear Gromacs users,
I run my simulation for 20ns and want to extract aromatic-aromatic
distance to see the stacking issue. But I am unable to get the value.
I have 24 molecules in my simulation and filled with solvents.
My index file is like that:
[ System ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62
'''''''
'''''''
'''''''
''''''
[ RING ]
19 20 21 22 23 24 25 26 27 28 29 30
32 34 37 38 39 40 42 44
This is the ring I created plane in the index file.
I used this command line
g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 20000 -o
DistPAP8HEP.xvg
but got the following like
I want to get the mean separation distance between two consecutive
polyaromatic rings along the axis of stacking
can someone help.
rob
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