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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>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Tue Apr 12 2011 - 22:00:02 PDT
