[gmx-users] question in pulling in gromacs 4.0
anirban polley
polley.anirban at gmail.com
Fri Mar 27 07:02:11 CET 2009
Hi ,
I want to pull a molecule from the membrane. My complete mdp file is
the following
;.........................................................................................................................................................................................................
; File 'mdout.mdp' was generated
; By user: psn (17109)
; On host: p690k
; At date: Fri Jul 23 12:43:31 2004
;
; VARIOUS PREPROCESSING OPTIONS =
title = lipid bilayer in water
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 500
dt = 0.002
nsteps = 1750000
; mode for center of mass motion removal =
comm-mode = Linear
; number of steps for center of mass motion removal =
nstcomm = 1
; group(s) for center of mass motion removal =
comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
;bd-temp = 300
;I have commute the above line as it has no exitance
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; 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 = 250
nstenergy = 250
; Output frequency and precision for xtc file =
nstxtcout = 0
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 =
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or no =
pbc = xyz
; nblist cut-off =
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME ;Reaction-Field
rcoulomb-switch = 0
rcoulomb = 1.0 ;2.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 80.0
epsilon_rf = 1
;I have done some thing new according to mannual and warnings and error
; Method for doing Van der Waals =
vdwtype = Cut-off
; cut-off lengths =
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = berendsen
; Groups to couple separately =
tc-grps = DPP SOL Na PIP
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1 0.1 0.1 0.1
ref_t = 310 310 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
;zero-temp_time = 0
;I have commute the above line as it has no exitance
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = all-bonds
; Type of constraint algorithm =
constraint_algorithm = lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SOR = no
; Relative tolerance of shake =
shake-tol = 0.0001
; 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
; Convert harmonic bonds to morse potentials =
morse = no
; ENERGY GROUP EXCLUSIONS =
; Pairs of energy groups for which all non-bonded interactions are excluded
=
energygrp_excl =
;............................................................................................................
;pulling
pull = umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = DPP
pull_group1 = PIP
pull_dim = N N Y
pull_k1 = 500
pull_kB1 = 500
pull_rate1 = 0.005
pull_vec1 = 0 0 -1
pull_init1 = -1.822
pull_nstxout = 100
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
=
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation =
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Orientation restraints: No or Yes =
orire = no
; Orientation restraints force constant and tau for time averaging =
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file =
nstorireout = 100
; Free energy control stuff =
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
; Electric fields =
; Format is number of terms (int) and for all terms an amplitude (real) =
; and a phase angle (real) =
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
..............................................................................................................................................................................................................................................................
Here, in the first step, there is no error or warning during the making of
.tpr file. But in the mdrun, after 3/4 steps, it crashes ans stop the MD
run. It gives the following error message:
Back Off! I just backed up dppc_pip2-ion_NPT_berendsen_md.edr to
./#dppc_pip2-ion_NPT_berendsen_md.edr.2#
starting mdrun 'Pure 122 DPPC and 1 PIP2 molecule bilayer with 3592 water
molecules'
1750000 steps, 3500.0 ps.
step 0
Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
.............................................
t = 500.004 ps: Water molecule starting at atom 10595 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 2, time 500.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 35.655980, max 638.714233 (between atoms 2849 and 2848)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
943 942 54.9 0.1498 3.0441 0.1530
942 941 88.6 0.1297 0.2327 0.1530
943 944 93.1 0.1291 20.4158 0.1530
944 945 93.6 0.1491 116.4443 0.1530
................................
Wrote pdb files with previous and current coordinates
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 21625 failed on node n0 (127.0.0.1) due to signal 11.
-----------------------------------------------------------------------------
/opt/torque/mom_priv/jobs/692.srclust.SC: line 20: unexpected EOF while
looking for matching `''
/opt/torque/mom_priv/jobs/692.srclust.SC: line 21: syntax error: unexpected
end of file
can anyone help me? where did I do mistake? Please
help me..
Regards,
Anirban
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