[gmx-users] DNA-protein complex distorted in vacuum simulation

[rahul dhakne]

Dear all Gromacs user,

   I minimized the energy of my DNA-protein complex with steep, l-bfgs
integrator, and then ran the mdrun with integrator = md in vacuum. Upto
energy minimization part it ran fine. When I submitted the minimized
structure for mdrun (vacuum), protein and DNA part jiggles around, also DNA
part is unwinding (breaking bond) and distort the complex. During
processing mdp file (gmx grompp -f md.mdp)I got one Note as follows

NOTE 1 [file topol.top, line 44]:
  System has non-zero total charge: -163.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

As the system is highly negatively charged it would have caused the
structure to distort or it could be  an artifact of visualization software??


I have used following parameters for MD simulation
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 100000     ; 1 *  100000 = 100ps
dt                  = 0.001             ; 1 fs
; Output control
nstxout                 = 1000          ; save coordinates every 10.0 ps
nstenergy               = 5000          ; save energies every 10.0 ps
nstlog                  = 5000          ; update log file every 10.0 ps

constraint_algorithm  = lincs       ; holonomic constraints
cutoff-scheme            = Verlet
ns_type                      = grid              ; search neighboring grid
cells
nstlist                          = 10            ; 20 fs, largely
irrelevant with Verlet scheme
rcoulomb                     = 1.0               ; short-range
electrostatic cutoff (in nm)
rvdw                            = 1.0               ; short-range van der
Waals cutoff (in nm)
coulombtype               = PME               ; Particle Mesh Ewald for
long-range electrostatics
constraints                  = none

For energy minimization I have used following parameters

; minim.mdp - used as input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent
minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps          = 1             ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist             = 10             ; Frequency to update the neighbor
list and long range forces
cutoff-scheme   = Verlet
ns_type             = grid              ; Method to determine neighbor list
(simple, grid)
coulombtype         = PME               ; Treatment of long range
electrostatic interactions
rcoulomb            = 1.0               ; Short-range electrostatic cut-off
rvdw                = 1.0               ; Short-range Van der Waals cut-off
pbc                     = xyz           ; Periodic Boundary Conditions
(yes/no)
constraints         = none

same parameters for L-BFGS with change in integrator


Could I use solvent for simulation or anything need to change
Any help would be much appreciated.
Thanking you in advance.


-
Rahul