On 6/19/13 9:25 AM, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.02
nsteps = 50000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = DPPC W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 50000
nstvout = 50000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 10000
nstenergy = 500
; Output frequency and precision for xtc file =
nstxtcout = 10000
xtc_precision = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =xtc-grps
=
; Selection of energy groups =
energygrps = DPPC W
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 325 325
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0
compressibility = 5e-6 0.0
ref_p = 0.0 0.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 325
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
What was the outcome of EM before this? What if you try NVT before NPT? Have
you tried reducing the timestep or the value of nstlist?
I would try everything with ref_p = 1.0 instead of zero to make sure you can get
a "normal" setup to work.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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