[gmx-users] Pull Code constant value

Vytautas Rakeviius vytautas1987 at yahoo.com
Tue Mar 28 16:06:35 CEST 2017

I suggest trial and error in quite short runs without wasting time on waiting for next day or so. Really large k can create segmentation faults or "cannonball into wall" like effects in MD movie.

    On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary <souparnoa91 at gmail.com> wrote:

 Hi all,

I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate this
value or it simply based on the trial-and-error method?

Also, what problems can take place if the value is large (huge, I guess)?


Souparno Adhikary
University of Calcutta.
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