[gmx-users] Re: Steered MD
schlesi at uni-mainz.de
Mon Oct 14 10:38:31 CEST 2013
First of all, sorry for the late answer.
More generally it is said the the rupture force depends logarithmically
on the loading rate (velocity times spring constant). -> So the
rup.force should also depend logarithmically on the spring constant (in
the simple bell modell).
Think the reason, why most people vary the velocity is, it is easier. If
you change the spring constant you also change the fluctuations in the
force (higher constant -> higher fluctuations) and it becomes way more
difficult to determine a rupture force.
For the dependence of the spring constant comes one paper to my mind:
S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten
Biophysical Journal Volume 72 April 1997 1568-1581
Molecular Dynamics Study of Unbinding of the Avidin-Biotin Complex
This might be a good starting point to find more recent publications on
Hope this helps you.
Am 09.10.2013 15:59, schrieb gmx-users-request at gromacs.org:
> Dear Gromacs Users,
> I am trying to look for some references regarding the SMD. I found one
> which tells about logarithmically dependency between the Rupture force
> (maximum pulling force) obtained from SMD and the pulling rate. Just
> wondering whether you are aware (or tested) the dependency between rupture
> force and harmonic spring constant?
More information about the gromacs.org_gmx-users