Justin A. Lemkul wrote:
Rebeca García Fandiño wrote:
Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1
and r_2).
I did not understand very well your last suggestion: "...if you want
reasonable error bars you will not lots of well-converged data".
Oops, that should have read "you will *need* lots of well-converged data."
Do you mean I will need also more windows besides extending the
simulations?
I doubt you need more windows. Likely you just need more time in each.
I think the problem could be also that the peptides I am using rotate
in the box and they do not remain flat one respect to the other. They
gyrate freely and some parts of their structure interact along the
pulling...
Interactions are part of the dissociation process and are not
problematic per se. But if you're trying to obtain only a
one-dimensional PMF then your rotation could be a problem. Is there
some reason you need a one-dimensional PMF and not a three-dimensional
PMF? What are you trying to achieve?
I should also add that if you're getting spurious interactions across periodic
boundaries, this is a problem. In that case, you need a different type of box,
like a dodecahedron for spherical symmetry.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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