Dear Dmitry,
Thank you for reply. Reviewing corresponding literature, I have seen that
the authors, who have used AMBER, obtain the force-extension curve by
differentiating the PMF curve. 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? I’m not sure that if
f=k*(x-x0) formula can be used to obtain a correct force-extension curve in
AMBER?
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
> > _______________________________________________
> > AMBER mailing list
> > 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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Received on Tue Apr 12 2011 - 23:30:03 PDT
