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: [email protected], [email protected]
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