[gmx-users] Justin paper 2010 pulling

[Adrian Devitt-Lee]

What do you mean by "different" peak forces?

Have you run multiple simulations with the same settings to see how much
your peak force varies? It may be that the force just has a high variance.

Best,
Adrian Devitt-Lee

On Wed, Sep 12, 2018 at 1:44 PM Rakesh Mishra <rockinbhu at gmail.com> wrote:

> Dear Justin
>
> It is totally surprised for me.
>  I am pulling the same system of bdna
> with the same constant velocity (0.005nm/ps).
>
> Case 1
> let for first case, When I am saving position coordinate (nstxtc ) in the
> interval of 4ps
> and saving energy coordinate in the interval of 4ps.
>
> Case 2
> In the second case of pulling of the same system with the same velocity, we
> save position
> coordinate in the interval of 4ps but we save energy coordinate in the
> interval of  10ps.
>
> Now in the output file of force.xvg for both case qualitative behaviour of
> diagram is same but
> Peak of the forces are much differ.  Why this saving frequency is affecting
> the peak value. While
> it is just saving the coordinates.
>
> We also found that, if we save energy coordinate with the same frequency
> and position
> coordinate with different frequency then, again peak value of forces are
> different.
> Which should not. Why it is happening. Can you clarify please.
>
>
> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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
> >
> > --
> > ==================================================
> >
> > 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
> > http://www.thelemkullab.com
> >
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> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
>
> *Phone n. +91 9473662491, +918777496532*
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