[gmx-users] finding Dihedrals with x2top

Ali Shomali ali.shomali111 at gmail.com
Sun Aug 27 14:00:56 CEST 2017

Dear Justin and all GROMACS users

I've faced a confusing problem in gromacs. when I'm using this instruction:
 for modeling a nanotube in my bilayer system. I found that the dihedral
number  which gromacs reports doesn't match the final dihdral number from
VMD or my own Code. but the " before cleaning " number is fine:

Before cleaning: 2900 pairs
Before cleaning: 2900 dihedrals
There are  760 proper dihedrals,    0 impropers, 1480 angles
          2180 pairs,      760 bonds and   520 atoms

so why GROMACS is deleting some dihedrlas?
if anyone can give me an advice I will be so thankful

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