[lammps-users] conjugate gradient and shake

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1

Hi,

I want to apply shake to all bond lengths in nafion polymer chain. But for energy minimization, say by conjugate gradient for example, required at the beginning, lammps says its error to use shake with energy minimization and its advised to use stiff spring constants to mimic shake.

Can anybody suggest if there’s any other solution possible or how stiff a force constant should be so that its reasonable? Dreiding force constant that I am using currently is 700 kcal/mol/A2 for harmonic or 70 kcal/mol for morse

Wouldn’t even using stiff force constant change the bond length, which otherwise I want to be at equilibrium bond length, to be maintained by shake in my MD after minimization?

Thanks in advance!

Regards,

Chetan

2

I'd just try various bond strengths and see what happens. The CG will adjust
the bond lengths slightly, but after you do the first step of dynamics
with SHAKE,
the bond lengths will be exactly their constraint value.

Steve

3

Dear Sir,

Thank you for your quick help!
I couldn't locate any provision for supplying constraint equilibrium value,
while using fix-shake, so is it that shake takes equilibrium value from bond
coeff command ?

Thank you,
Chetan

4

I believe that the shake implementation in LAMMPS allows only for small
clusters of atoms to be constrained. SHAKing all bonds in a polymer
backbone might not work.

  Lutz

5

yes, SHAKE operates on the bond length specified in the bond_coeff command

Steve