[gmx-users] Justin paper 2010 pulling

Rakesh Mishra rockinbhu at gmail.com
Tue Sep 4 17:44:06 CEST 2018

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.

Hoping your response.


*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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