[gmx-users] pulling of molecule in GROMACS 4.03
anirban polley
polley.anirban at gmail.com
Wed Mar 25 12:11:12 CET 2009
Dear Sir,
I want to pull a molecule called PRO from the lipid membrane
DPP. To do this I have written the .mdp file as following from the help of
gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file,
it says that "segmentation fault".
Can you please write the correct .mdp file for the pulling? It
will be really a great help to me.
Thanking you,
Anirban
;
; 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 PRO
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1 0.1 0.1
ref_t = 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 =
continuation = yes
;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
;COM pulling
pull = umbrella
pull_geometry = cylinder
pull_dim = N N Y
pull_r1 = 1
pull_r0 = 1
;pull_constr_tot = 1e-6
pull_start = yes
pull_nstxout = 10
pull_nstfout = 1
pull_ngroups = 1
;name of reference group
pull_group0 = DPP
;pull_weights = 0
;name of pull group
pull_group1 = PIP
;pull_weights = 0
pull_vec1 = 0.0 0.0 -1
;ref. distance at t=0
pull_init1 =
;rate of change of ref. gr. [nm/ps]
pull_rate1 = 0.0005
;force constant [KJ mol^-1 nm^-2]
pull_k1 = 500
;pull_kB1 =
; ENERGY GROUP EXCLUSIONS =
; Pairs of energy groups for which all non-bonded interactions are excluded
=
energygrp_excl =
; 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
userreal4 = 0
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