[gmx-users] Umbrella sampling: window distance - harmonic force constant
J.Hermann at lrz.tu-muenchen.de
Wed Mar 28 11:00:28 CEST 2018
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
>> 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.
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Tel: +49 8928915730
Fax: +49 8928915714
Email: j.hermann at lrz.tum.de
More information about the gromacs.org_gmx-users