On Wed, Apr 13, 2011 at 12:12 PM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> > Reviewing corresponding literature, I have seen that
> > the authors, who have used AMBER, obtain the force-extension curve by
> > differentiating the PMF curve.
>
> I will appreciate if you give a link to that paper.
>
> Two papers for DNA pulling:
- S.A. Harris et al., Molecular Dynamics Simulations of Duplex Stretching
Reveal the Importance of Entropy in Determining the Biomechanical Properties
of DNA, Biophysical J., 88, 2005, 1684–1691.
- S. Piana, Structure and energy of a DNA dodecamer under tensile load,
Nucleic Acids Research, 2005, 33, 7029–7038.
> However, it seems that the authors, who have
> > used other packages such as Gromacs and NAMD, usually obtain the
> > force-extension curve directly from SMD (i.e. the spring force formula).
> I
> > don’t know that whether the different methods employed in AMBER and the
> > other packages have leaded to this difference or not?
>
> Someone can correct the following. I suppose you try to compare
> results from atomic force microscopy experiment with SMD results. Thus
> you try to mimic AFM technique by SMD pulling. First of all you can
> try to compare directly observed forces and it is easy to do. If SMD
> force is similar to AFM force you won. If SMD force is much larger
> than AFM one I can conclude that SMD can not correctly reproduce the
> value of force, work and energy. If SMD force is not much larger than
> AFM one you can try to reconstruct PMF from multiple SMD pullings
> (through Jarzynski averaging) and to recalculate force from that PMF.
> In this way you try to subtract dissipative work thus you will get the
> lower force value.
>
> > I’m not sure that if
> > f=k*(x-x0) formula can be used to obtain a correct force-extension curve
> in
> > AMBER?
>
> Force values f=2*rk2*(x-x0) are just printed in the third column of
> output dist_vs_ t file.
> Over the one MD step force value is constant.
>
> > On Wed, Apr 13, 2011 at 9:01 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> >
> >> Hello, generally time scale of SMD is much shorter than time of
> >> experiment. Sо it can be difficult to compare the forces directly.
> >>
> >> Please note that rk2 parameter used in dist.RST file (from which
> >> restraint information will be read) is not k but k/2 in relation to
> >> f=k*(x-x0) formula (i.e. k = 2*rk2).
> >>
> >> On Tue, Apr 12, 2011 at 9:17 PM, Ali M. Naserian-Nik
> >> <naseriannik.gmail.com> wrote:
> >> > Hi all,
> >> >
> >> >
> >> > I hope that the details of steered MD method employed in AMBER be
> >> explained
> >> > more for non-professional users through the manual. During a pulling
> >> > simulation, such as DNA pulling, a force-extension curve can be
> obtained
> >> > from the output file which is generated by setting jar=1 (i.e.
> k*(x-x0)
> >> vs.
> >> > x). I’m not sure that if this curve can be compared with a similar
> curve
> >> > which is obtained from an experimental simulation (assuming the time
> >> scale
> >> > in the two cases are nearly equal); or firstly the potential of mean
> >> force
> >> > must be calculated and then forces obtained as derivative of the PMF?
> >> >
> >> > Any comments would be greatly appreciated.
> >> >
> >> >
> >> >
> >> > Thanks in advance
> >> >
> >> > --
> >> > Ali
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> Dmitry Nilov,
> >> Faculty of Bioengineering and Bioinformatics,
> >> Lomonosov Moscow State University
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Ali
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dmitry Nilov,
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
>
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>
--
Ali
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Received on Wed Apr 13 2011 - 01:30:03 PDT
