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

[tarak karmakar]

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 ?

Thanks
Tarak

On Fri, Oct 12, 2012 at 8:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/12/12 10:39 AM, Dr. Vitaly Chaban wrote:
>>>
>>>
>>> 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 .
>>
>
> For what it's worth, I've employed a similar setup as the OP and it worked
> quite well, though there are probably several ways to address this issue.  I
> can think of at least four.
>
>
> -Justin
>
> --
> ========================================
>
> 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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-- 
Tarak