[gmx-users] DNA didnot wrap around CNT

[Justin A. Lemkul]

Siamkhanthang Neihsial wrote:
> Hi friends,
>  
>         I have a DNA sequence (5'-GAG TCT GTG GAG GAG GTA GTC-3') and a 
> CNT(6,5) of 90 Angstroms in length. I kept the DNA & CNT at a distance 
> of 1 angstrom. Solvents molecules(water) inside CNT are removed at a 
> radius of CNT at 4.2 . Equilibration at 1000 steps,  results in 
> diminished quality of CNT (like bonds between carbons are no more 
> visible!), i repeat equilibration with larger steps( 5000), the same 

Bonds cannot break or form in molecular mechanics.  Whatever you're seeing is a 
visualization artifact.

> problem result. Also,the DNA is suppose to wraped around the CNT, but it 
> didnot seems to happen. I am using GROMACS. Any help will be highly 
> appreciated.

If your model is not reproducing the correct behavior, then there's probably 
something wrong with the model.

> My equil.mdp file is
> 

What you've got here is an energy minimization, not equilibration, input file. 
No large-scale changes are going to happen during EM.  I would suggest you go 
through some tutorial material to understand a proper Gromacs workflow in order 
to run actual MD.

-Justin

> ; LINES STARTING WITH ';' ARE COMMENTS
> title                 = Minimization of "-----"     ; Title of run
> ; The following lines tell the program the standard locations where to 
> find certain files
> Define            =-Dflexible
> cpp                 = cpp    ; Preprocessor
> 
> ; Parameters describing what to do, when to stop and what to save
> integrator       = steep      ; Algorithm (steep = steepest descent 
> minimization)
> emtol              = 1.0        ; Stop minimization when the maximum 
> force < 1.0 kJ/mol
> nsteps            = 1000        ; Maximum number of (minimization) steps 
> to perform
> nstenergy       = 5        ; Write energies to disk every nstenergy steps
> nstxtcout        = 10        ; Write coordinates to disk every nstxtcout 
> steps
> xtc_grps         = Protein SOL     ; Which coordinate group(s) to write 
> to disk
> energygrps     = Protein SOL     ; Which energy group(s) to write to disk
> 
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist              = 5        ; Frequency to update the neighbor list 
> and long range forces
> ns_type           = simple    ; Method to determine neighbor list 
> (simple, grid)
> coulombtype    = PME-switch       ; Treatment of long range 
> electrostatic interactions
> rcoulomb          = 0.9        ; long range electrostatic cut-off
> rlist                  = 1.0        ; Cut-off for making neighbor list 
> (short range forces)
> vdwtype          = Shift
> rvdw                = 0.9        ; long range Van der Waals cut-off
> constraints      = all-bonds        ; Bond types to replace by constraints
> pbc                  = xyz        ; Periodic Boundary Conditions (yes/no)
> constraint_algorithm=LINCS
> lincs_order     =4
> lincs_iter        =2
> periodic_molecules = yes
> nstcomm         = 1
> comm_mode  = Linear
> comm_grps    = Protein SOL
> 
> -- 
> Best Regards,
> 
> Siam
> Theoretical Sciences Unit,
> JNCASR,
> (Lab) +91-080-2208-2581, (M) +91-8971001405
> e-mail: sktn06 at gmail.com <mailto:sktn06 at gmail.com>, siam at jncasr.ac.in 
> <mailto:siam at jncasr.ac.in>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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