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

[Dr. Vitaly Chaban]

>
> 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 !!

Introducing constraints between non-covalently bound sites may (and
often does in practice) result in the instability of your system and
may require smaller time-step.

Personally, I would introduce morse potential with a weak force
constant for the same task .


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark