[gmx-users] LINCS metal-ligand bonds

tarak karmakar tarak20489 at gmail.com
Fri Oct 12 08:42:09 CEST 2012

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.


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