Just to make clear, there is potentially critical difference between
ibelly and ntr
ibelly is a CONSTRAINT, which means the atoms/groups picked do not move
at ALL. There are no forces on them, since they are zeroed-out at every
step in MD o minimization.n
ntr is a RESTRAINT, which means the atoms/groups picked are allowed to
move from the target coordinates, by an amount associated with the
strenght of the restraint strength.
Which one to use/when can depend on the user's goals, but they are
technically NOT equivalent.
adrian
On 7/26/16 12:13 PM, Barbault Florent wrote:
> Dear Saman,
>
> Yes it is true, harmonic restraints (ntr) should be the unique
> solution when you want to fix coordinates. However, in some few cases
> I find belly useful like when I do simulations of biosensors (a DNA
> linked to a metalic surface, for example). If you work with isotropic
> conditions with "classical" atoms you might only need ntr.
>
> Best,
> Florent
>
>
>
> On Tue, 26 Jul 2016 09:38:42 +0000 (UTC)
> Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>> Dear all,
>> Is it true that the use of ntr is better than ibelly to completely
>> freeze certain groups during molecular dynamics simulation?
>>
>> Best Regards, Saman
>>
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> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Associate professor
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://florentbarbault.wordpress.com/
> tel : (33) 01-57-27-68-61
> e-mail : florent.barbault.univ-paris-diderot.fr
> -------------------------------------------------
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jul 26 2016 - 03:30:03 PDT
