[gmx-users] pull=constraint gives zero forces
schlesi at uni-mainz.de
Thu Oct 11 10:21:55 CEST 2012
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.
Am 10.10.2012 18:41, schrieb gmx-users-request at 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,
> -- 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.
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