[gmx-users] Making covalent bonds between protein subunits
k.a.feenstra at chem.rug.nl
Thu Oct 25 11:13:29 CEST 2001
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.
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).
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| _ _ ___,| Anton Feenstra Dept. of Biophysical Chemistry|
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