[gmx-users] Justin paper 2010 pulling

Justin Lemkul jalemkul at vt.edu
Thu Sep 6 13:50:35 CEST 2018

On 9/6/18 2:29 AM, Rakesh Mishra wrote:
> While I have purely physics background.
> But, In my thinking, there are hydrogen bonds (electrostatic attractive
> interaction)
> between bp of  both the strands of DNA/RNA  which are perpendicular to
> helix direction.
> And the other thing you have chosen very fast velocity like (0.01, 0.001,
> 0.005 ).
> This can also be the reason of smoothness. But can you tell me one thing
> please,the
> value of spring constant of biasing that you have taken (k= 1000), is
> standard or not . If this value can be taken for peptide pulling .  Can
> this value of
> spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
> not .

There is no such thing as a "standard" force constant for pulling.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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