[gmx-users] Making covalent bonds between protein subunits

[K.A.Feenstra]

Volker Knecht wrote:
> 
> Hi Chris,
> 
> an alternative solution: Instead of specifying new covalent bonds, you could define *distance restraints* on the calcium and monomer atoms (see
> GROMACS manual). These are, roughly speaking, also harmonic potentials. Maybe they work better.

Two remarks: 
1) depending on the parameters, distance restraints can be exactly harmonic potentials.
2) bonds usually are *not* represented by harmonic potentials, but by constraints
   (don't confuse constraint and restraint, a constraint is a fixed distance w/o potential).
But, I would think Volkers' suggestion is a good one (let's hope it works).

-- 
Groetjes,

Anton
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|  _   _  ___,| Anton Feenstra        Dept. of Biophysical Chemistry|
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