[gmx-users] Justin paper 2010 pulling

Rakesh Mishra rockinbhu at gmail.com
Wed Sep 5 07:50:06 CEST 2018

So that means

It is may be due to the  difference in the type of interaction.

and I can not understand your this statement "you have to contend with
forces principally acting perpendicular to the direction of the bias"

On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
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> 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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