[gmx-users] LINCS metal-ligand bonds

[Justin Lemkul]

On 10/12/12 2:42 AM, tarak karmakar wrote:
> Dear ALL,
>
> In my protein I need to constraint the length between the Metal and
> the N of Histidine residues.  In the .rtp file I didn't specify this
> Mn-N connectivity; these are more or less coordinate bonds.  So to do
> that I specified the Mn, N-atom indices  and the corresponding lengths
> in the topology file, part of it is given below
>
>
> [ constraints ]
> ;  index1  index2   funct          length(nm)
>      6062   6063       1        0.11490000000
>      6062   6064       1        0.11490000000
>      6060   4309       1        0.21000000000
>      6060   4268       1        0.22700000000
>      6060   4979       1        0.22600000000
>
>
>   In the .mdp file I have included the following lines
>
>
> constraints             = h-bonds       ; covalent h-bonds constraints
> constraint_algorithm    = LINCS         ; LINear Constraint Solver
> continuation            = yes           ; apply constraints to the
> start configuration
> lincs_order             = 4             ; highest order in the
> expansion of the contraint coupling matrix
> lincs_iter              = 1             ; number of iterations to
> correct for rotational lengthening
> lincs_warnangle         = 30            ; [degrees] maximum angle that
> a bond can rotate before LINCS will complain
>
>
> [ I followed the above mentioned protocol and I see Mn-N distances are
> not changing during the simulation, so served my purpose.]
>
> So for all sorts of specified constraints (H-covalent bonds, Mn-N
> coordinate bonds), MD will make use of LINCS algorithm !! . But my
> query is about whether LINCS will be equally applicable as that of for
> covalent bonds in constraining Mn-N distances where the real(?)
> bonds(connectivity) don't exist !!
>
>
>
> Differentiating bond types ( covalent or coordinate) by means of
> connectivity information.
>

There is no such differentiation, at least in normal molecular mechanics force 
fields.  You're telling mdrun that there are constraints in the system, and it's 
applying them.  It has no intuition as to the chemical nature of these 
bonds/constraints.  You can constrain any distance you like in a system via 
LINCS or SHAKE (chosen in the .mdp file, LINCS is default).

-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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