[gmx-users] Maximum Force constant for Position Restraints

[David van der Spoel]

On 2015-04-21 21:40, Alex wrote:
> No, it does not depend on the system content, aside from the mass of the
> particle.
> For a simulation requiring numerical integration in time, there is a limit,
> and I just estimated it above. For the real world, the limit is that
> there's no such thing as a harmonic position restraint. :)
> If you want to be really hardcore about it, and still assume there _is_
> such a thing as harmonic restraints, then the "timestep" of the real world
> is your Planck's time. :)
But it boils down to that if you make the force constant very large you 
need to make the time step short too which may not be what you want.
>
> Alex
>
> On Tue, Apr 21, 2015 at 1:36 PM, Marcelo Depólo <marcelodepolo at gmail.com>
> wrote:
>
>> Thanks Alex. But then, theoretically, is there no limit? All depends on
>> your system's content, right?
>>
>> 2015-04-21 16:16 GMT-03:00 Alex <nedomacho at gmail.com>:
>>
>>> Correction: tau/pi on the left for the highest value and 5*tau/pi for the
>>> 10 x period suggestion above.
>>>
>>> On Tue, Apr 21, 2015 at 1:13 PM, Alex <nedomacho at gmail.com> wrote:
>>>
>>>> I think this can be estimated from a general physical argument. The
>>>> absolute max in my opinion should come from
>>>> 4*pi*tau = sqrt(m/k), where m is the mass of the lightest restrained
>>>> particle in the system, k is the constant you seek, and tau is the
>>>> timestep.
>>>> The coefficient is four because of the Nyquist theorem. I believe GMX
>>>> tests for high vibrational frequencies according to 20*pi*tau on the
>> left
>>>> (ten times the period).
>>>>
>>>> Hope this helps.
>>>>
>>>> Alex
>>>>
>>>>
>>>> On Tue, Apr 21, 2015 at 1:02 PM, Marcelo Depólo <
>> marcelodepolo at gmail.com
>>>>
>>>> wrote:
>>>>
>>>>> Hi guys!
>>>>>
>>>>> Is there a maximum value of Force Constant for Position restraints?
>>>>> Reading
>>>>> the Manual I could only find the default and the equation to describe
>>> it.
>>>>>
>>>>> Best,
>>>>> --
>>>>> Marcelo Depólo Polêto
>>>>> Group of Structural Bioinformatics - Center of Biotechnology
>>>>> Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
>>>>> B.Sc. Biochemistry - University of Viçosa (Brazil)
>>>>> --
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>>>>
>>>>
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>>
>>
>> --
>> Marcelo Depólo Polêto
>> Group of Structural Bioinformatics - Center of Biotechnology
>> Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
>> B.Sc. Biochemistry - University of Viçosa (Brazil)
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se