rainy...@yahoo.com wrote:
Hi Justin,
Sorry I didn't include all of my md.mdp file, as it is quite long :). I
have included as a reference below. I've taken a look at the log file,
but I'm not really sure what I should be looking for so to identify what
is causing my system to blow up? Should I start with the energies (see
below)?
Any messages in the log file would be fairly obvious that something is going
wrong (LINCS warnings, extremely high temperature, energy, etc).
Finally, I've read through the "Blowing up" link you sent me. Taking it
into consideration, do you suggest that I lower my timestep in my em.mdp
file? It's already at dt = 0.02?
The dt parameter is for MD only; it is irrelevant in EM. Was EM successful on
your system? Have you done any equilibration prior to running unrestrained MD?
For the MD, you shouldn't have to reduce the value of dt any further. 20 fs
is the lowest that the MARTINI developers recommend.
-Justin
Thanks!
Lily
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*log file
*++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.030283 453 454 0.008216
After LINCS 0.000040 1278 1276 0.000011
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
4.22829e+03 7.72020e+03 -6.51083e+06 5.87935e+01 -6.49883e+06
Kinetic En. Total Energy Temperature Pressure (bar)
9.04109e+05 -5.59472e+06 3.10086e+02 -2.18809e+03
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*md.mdp file*
integrator = md
; start time and timestep in ps
tinit = 0
dt = 0.020
;nsteps = 10000 ; initial step
nsteps = 10000000 ; 200 ns @ dt=0.02
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 10000 ; frame every 150 ps
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 = PROTEIN W ION
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; 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 =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; 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 =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = PROTEIN SOLVENT
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 310
gen_seed = 1
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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