See the SHAKE algorithm in the manual.
Especially equation (3.98)
-> G_i = \sum_k \lambda_k * (\partial \sigma_k)/(\partial r_i)
where G_i is the constraint force
\sigma_k are the equations for the constraints
and \lambda_k is the lagrange multiplier
'Understanding molecular simulation' (D. Frenkel, B. Smit)
gives these equations for bond-constraints as
\sigma = r_ij^2 - d_ij^2
where r_ij is the real distance, and d_ij to one to which one wants to
constrain the bond length
from this \lambda_k would correspond to a force constant.
Greetings
Thomas
Am 10.10.2012 18:41, schrieb gmx-users-requ...@gromacs.org:
How can there be forces for holonomic constraints? Is this described by an
equation in the manual?
Just because there are values in the pullf.xvg file does not mean that these
values are forces.
If they are forces, what is the force constant and what is the equation that
defines this force?
Thank you,
Chris.
-- original message --
But for GMX 4.0.7 there are forces in the pullf.xvg. The forces which
arise rom the contraint the hold the two groups fixed. I use them for
thermodynamic integration...
I use the following mdp-parameters, probably this gives you an idea what
you might make different:
; AFM OPTIONS
pull = constraint
pull_geometry = distance
pull_dim = Y Y Y
pull_start = yes
pull_nstfout = 10
pull_nstxout = 500000
pull_ngroups = 1
pull_group0 = REF
pull_group1 = ZUG
pull_rate1 = 0.000
pull_init1 = 0.000
pull_constr_tol = 1e-06
But as Chris said, better post the complete mdp-file (probably for both
GMX 4.0.7 and 4.5.x) so we can comment on them.
Grettings
Thomas
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