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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