Hello everybody,
I have a basic question concerning SMD and PMF. What are the units for
the force and work printed in the output?
Regards
Florent
On Wed, 13 Apr 2011 11:42:25 +0400
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.
>
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://florentbarbault.wordpress.com/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr
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Received on Wed Apr 13 2011 - 02:00:04 PDT
