Harmonic restraints with certain spring constants

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1

Dear all,

I have a protein molecule in a box of solvent. I want the protein molecule to be flexible through harmonic restraints that let the atoms vibrate around their
initial positions. I have only the spring constant (k) and not the equilibrium bond length (r0). Is it possible to somehow use a bond_coeff command with only specifying spring constant (k = same for all type of bonds) and consider the equilibrium distance from the position of atoms in the coordinate file. If not, is there any other way to do that ?.

It would be very grateful if someone could help me regarding this.

Thanks in advance.

2

Dear all,

I have a protein molecule in a box of solvent. I want the protein molecule
to be flexible through harmonic restraints that let the atoms vibrate
around their
initial positions. I have only the spring constant (k) and not the
equilibrium bond length (r0). Is it possible to somehow use a bond_coeff
command with only specifying spring constant (k = same for all type of
bonds) and consider the equilibrium distance from the position of atoms in
the coordinate file. If not, is there any other way to do that ?.

​if you want position restraints, it does not make sense to mess around
with bonds (from where to where?)​. instead use fix spring/self. that does
exactly that.

axel.

3

Dear Axel,

Thanks for your valuable suggestion. Yes, It does what I wanted.

Kind regards
Debdas