> 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.
> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Dmitry Nilov,
>> Faculty of Bioengineering and Bioinformatics,
>> Lomonosov Moscow State University
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> 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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Received on Wed Apr 13 2011 - 01:00:03 PDT
