[gmx-users] Energies in MM scanning using gmx

[fantasticqhl]

Dear all,

But I have questions about the energies calculated by GMX for bonds and
angles scanning.

For example, a series of conformations of one system should be generated for
a bond scanning, the only difference in geometry of these conformations is
the bond length A---B.
However, when I set the force constant as 0 for bond A---B, the bond
energies is not a flat line as the bond length changes, in principle, it
should be a flat line, but it is not.

<http://gromacs.5086.x6.nabble.com/file/n5010274/bond_1FF.png> 


This is an example I got for my system. Could some tell me how to explain
the energy differences? Thanks very much!

All the best,
qh 





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