[gmx-users] DNA-protein complex

[Urszula Uciechowska]

The force field that I used was ambe99bsc0, and my input file was:
; 7.3.3 Run Control
integrator              = md                    ; md integrator
tinit                   = 0                     ; [ps] starting time for run
dt                      = 0.002                 ; [ps] time step for
integration
nsteps                  = 5000000               ; maximum number of steps
to integrate, 0.002 * 2,500,000 = 5,000 ps
comm_mode               = Linear                ; remove center of mass
translation
nstcomm                 = 1                     ; [steps] frequency of
mass motion removal
comm_grps               = Protein Non-Protein   ; group(s) for center of
mass motion removal

; 7.3.8 Output Control
nstxout                 = 2500000       ; [steps] freq to write
coordinates to trajectory
nstvout                 = 2500000       ; [steps] freq to write velocities
to trajectory
nstfout                 = 2500000       ; [steps] freq to write forces to
trajectory
nstlog                  = 100           ; [steps] freq to write energies
to log file
nstenergy               = 500           ; [steps] freq to write energies
to energy file
nstxtcout               = 500           ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision           = 1000          ; [real] precision to write xtc
trajectory
xtc_grps                = System        ; group(s) to write to xtc trajectory
energygrps              = System        ; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist                 = 1             ; [steps] freq to update neighbor
list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions in
all directions
rlist                   = 0.8           ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 0.8           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = cut-off       ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 0.8           ; [nm] distance for LJ cut-off
DispCorr                = EnerPres      ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing          = 0.12          ; [nm] grid spacing for FFT grid
when using PME
pme_order               = 4             ; interpolation order for PME, 4 =
cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl                  = v-rescale                     ; temperature
coupling with Nose-Hoover ensemble
tc_grps                 = Protein    Non-Protein        ; groups to couple
seperately to temperature bath
tau_t                   = 0.1        0.1                ; [ps] time
constant for coupling
ref_t                   = 310        310                ; [K] reference
temperature for coupling

; 7.3.15 Pressure Coupling
pcoupl                  = parrinello-rahman     ; pressure coupling where
box vectors are variable
pcoupltype              = isotropic             ; pressure coupling in
x-y-z directions
tau_p                   = 2.0                   ; [ps] time constant for
coupling
compressibility         = 4.5e-5                ; [bar^-1] compressibility
ref_p                   = 1.0                   ; [bar] reference pressure
for coupling

; 7.3.17 Velocity Generation
gen_vel                 = no            ; velocity generation turned off
; 7.3.18 Bonds
constraints             = all-bonds     ; convert all bonds to constraints
constraint_algorithm    = LINCS         ; LINear Constraint Solver
continuation            = yes           ; apply constraints to the start
configuration
lincs_order             = 4             ; highest order in the expansion
of the contraint coupling matrix
lincs_iter              = 1             ; number of iterations to correct
for rotational lengthening
lincs_warnangle         = 30            ; [degrees] maximum angle that a
bond can rotate before LINCS will complain

best regards
Urszula Uciechowska




> 2015-03-17 14:35 GMT-03:00 Urszula Uciechowska <
> urszula.uciechowska at biotech.ug.edu.pl>:
>
>>
>>
>> Hi,
>>
>> I am running MD for dsDNA-protein complex. After 50ns I observed that
>> the
>> DNA is unwinding. What did go wrong? Should I have changed something in
>> my
>> input file?
>>
>> You might want to send your input files, so as your force field that you
> have choose. It is hard to say anything without more details.
> Also, what do you mean by 'unwinding'? Could you be more specific?
>
>
>> Thank you in advance for your suggestions.
>> best regards
>> Urszula
>>
>
> Cheers!
> --
> Marcelo Depólo Polêto
> B.Sc. Biochemistry - University of Viçosa (Brazil)
> --
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University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


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