GROMACS version:
GROMACS modification: Yes/No
Dead all
I would like to determine the angles between two ssdna base rings stacked on top of each other
I tried various methods but ssdna base step parameters are not calculated as there is no software yet.
I tried the x3dna and the biobb but they require double strand for calculation.
I am trying the gromacs now but the problem coming are several that are already reported but the solutions I cannot understand.
I create an index file like this with atom numbers
A
1 2 3
B
2 3 5
The error the gms trows is number divisible by 3 .
I have created triplets as indicated in help.
Is it wrong to give atom numbers?
The other issue was when I write -g1 as plane.
The error is group 1 and 2 should be the same selection.
Can anyone explain the situation and how to resolve it.
I am grateful for any idea that can come my way.
Tnank you