[gmx-users] Justin paper 2010 pulling

Justin Lemkul jalemkul at vt.edu
Tue Sep 4 19:24:59 CEST 2018

On 9/4/18 11:44 AM, Rakesh Mishra wrote:
> Dear Justin,
> Seriously I want to remove my confusion.
> I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
> Where you have studied stability of Alzheimer. I don't want to ask about
> umbrella sampling used for the calculation of PMF.
> But , before the calculation of PMF , you
> have obtained simple dissociation using your  pulling protocol of gromacs
> with constant velocity simulation at three different velocities.  I am
> surprised that you have followed the obvious protocol
> of minimization the nvt the npt and then 100ns md production. then you took
> final structure of 100ns and made new box for pulling  and followed the
> same minimisation and npt for short time. After this you did pulling along
> only one direction (one reaction coordinate) .
> I am surprised that how such a smooth force/time data you have obtained for
> all the velocities (0.01,0.001,0.005) . I am asking because for my simple
> 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed
> one end (say 5') of first strand and pulling opposite end (5') of second
> strand along the helical direction of the system. Here, I am getting
> force/time (in the .xvg ) data which is qualitatively similar behaviour
> like yours i.e.  initially increasing then reach to maximum and then
> decreasing almost becomes to zero value. But , In mine case during initial
> time of pulling force is also negative as well large fluctuation of force .
> But not such a smooth Variation of force/time like your in this paper. In
> your case, force is increasing like linearly in the initial and reaches the
> maximum and then start to decrease.  There is no problem to
> clarify the peak of force (maximum force) in your pulling (above mentioned
> paper). While in our case its very difficult to clarify the peak force due
> to large fluctuation in value.
> Can you please tell me something about the reason. Its smoothness is now
> became headache for my calculation in all the case of pulling.

There is no reason to think that your outcome and mine should look 
anything alike. Pulling apart two proteins that interact in the way the 
peptides do in a protofibril is much simpler than the intertwined nature 
of a DNA or RNA duplex. If you pull along the helix axis, you have to 
contend with forces principally acting perpendicular to the direction of 
the bias, as well as the fact that the strands have to slide past one 
another, requiring major distortion of the helix and/or frictional 
forces due to the individual strands unwinding from one another.



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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