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: [email protected] <mailto:[email protected]>, [email protected]
<mailto:[email protected]>
--
========================================
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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