kcal/mol-A and kcal/mol
On Wed, Apr 13, 2011 at 12:55 PM, Barbault Florent
<florent.barbault.univ-paris-diderot.fr> wrote:
> 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
>>>>
>>>> _______________________________________________
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>>>> 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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>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Apr 13 2011 - 02:30:03 PDT
