[gmx-users] harmonic potential on the distance between two atoms
shirlinw at yahoo.com
Tue Feb 14 22:53:29 CET 2006
I am doing simulation on a single peptide (352 atoms)
solvated in a box of water. I want to apply a harmonic
interaction between two atoms on the peptide which are
not chemically bonded. So I add a section in the top
; ai aj funct b0 kb
1 349 6 3.0e-01 1.0e+01
My mdrun stopped right after started, leaving quite a
few step??.pdb files. The MD log file say:
There were 2 inconsistent shifts. Check your topology.
If I don't include the above section in the top file,
it runs perfectly. I have also tried to vary the value
of b0 and kb, still failed.
Could someone tell me what is wrong with my way of
implementing harmonic potential?
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