Okay. Thanks Justin!
On 27.03.2018 21:12, Justin Lemkul wrote:
On 3/27/18 4:44 AM, Hermann, Johannes wrote:
Dear All, dear Justin,
I am playing around with my umbrella sampling setup and I was looking
at your paper which you linked in your umbrella sampling tutorial
("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using
Molecular Dynamics").
Up to a distance of 2nm you use a 0.1nm spacing, beyond a 0.2nm
spacing. Which harmonic force constant pull_coord1_k do you use for
the 0.1nm spacing? In comparison to the 0.2nm spacing, where
pull_coord1_k=1000.
Is there a general rule of thumb between window distance and force
constant? Or is it always try and error while checking the histograms?
You can set the value of k based on experimental methods or somewhat
ad hoc, but then yes, you have to check overlap. I don't know of any
useful way of trying to predict how the intermolecular forces in the
system will respond in such a way that you can exactly say a priori
how to set up the windows.
-Justin
--
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714
Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
