[gmx-users] Re: LINCS metal-ligand bonds

[Justin Lemkul]

On 10/12/12 2:50 PM, tarak karmakar wrote:
> Thanks Justin & Chaban.
>
> Even I did the simulation for 3 ns and it worked well.
> Now the issue in my case is , while I was not imposing the M-N
> constraints, the metal was rattling around (little bit)  and the
> histidine residues were moving back and forth (elongation of M-Nhis
> length). So I employed constraints to keep them in peace. But I'm bit
> worried about the dynamics of the entire protein. I'm not sure how
> accurate results these will produce if I impose these sorts of
> approximations. Any idea ? Any reference where people have followed
> the same ?
>

Anything you do is going to suffer from the fact that it's an approximation 
since MM force fields are not going to preserve coordination geometry for these 
ions.  A constraint is very rigid, but on average, probably describes correct 
behavior.  A harmonic interaction is defined by the force constant, but you'll 
have a hard time defining proper parameters for that, too.  A distance restraint 
suffers from a similar interaction regarding how "hard" the interaction is. 
Surely a few minutes searching will turn up pertinent literature.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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