[gmx-users] DNA didnot wrap around CNT

[Siamkhanthang Neihsial]

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 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.
My equil.mdp file is

; 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, siam at jncasr.ac.in
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