Dear Sir,<br>
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".<br>
Can you please write the correct .mdp file for the pulling? It will be
really a great help to me.<br>
Thanking you,<br>
Anirban<br>
<br>
;<br>
; File 'mdout.mdp' was generated<br>
; By user: psn (17109)<br>
; On host: p690k<br>
; At date: Fri Jul 23 12:43:31 2004<br>
;<br>
<br>
; VARIOUS PREPROCESSING OPTIONS =<br>
title
= lipid bilayer in water<br>
cpp
= /lib/cpp<br>
include =<br>
define =<br>
<br>
; RUN CONTROL PARAMETERS =<br>
integrator = md<br>
; start time and timestep in ps =<br>
tinit = 500<br>
dt
= 0.002<br>
nsteps = 1750000<br>
; mode for center of mass motion removal =<br>
comm-mode = Linear<br>
; number of steps for center of mass motion removal =<br>
nstcomm = 1<br>
; group(s) for center of mass motion removal =<br>
comm-grps =<br>
<br>
; LANGEVIN DYNAMICS OPTIONS =<br>
; Temperature, friction coefficient (amu/ps) and random seed =<br>
;bd-temp = 300<br>
;I have commute the above line as it has no exitance<br>
bd-fric = 0<br>
ld-seed = 1993<br>
<br>
; ENERGY MINIMIZATION OPTIONS =<br>
; Force tolerance and initial step-size =<br>
emtol = 100<br>
emstep = 0.01<br>
; Max number of iterations in relax_shells =<br>
niter = 20<br>
; Step size (1/ps^2) for minimization of flexible constraints =<br>
fcstep = 0<br>
; Frequency of steepest descents steps when doing CG =<br>
nstcgsteep = 1000<br>
<br>
; OUTPUT CONTROL OPTIONS =<br>
; Output frequency for coords (x), velocities (v) and forces (f) =<br>
nstxout = 5000<br>
nstvout = 5000<br>
nstfout = 0<br>
; Output frequency for energies to log file and energy file =<br>
nstlog = 250<br>
nstenergy = 250<br>
; Output frequency and precision for xtc file =<br>
nstxtcout = 0<br>
xtc-precision = 1000<br>
; This selects the subset of atoms for the xtc file. You can =<br>
; select multiple groups. By default all atoms will be written. =<br>
xtc-grps =<br>
; Selection of energy groups =<br>
energygrps =<br>
<br>
; NEIGHBORSEARCHING PARAMETERS =<br>
; nblist update frequency =<br>
nstlist = 10<br>
; ns algorithm (simple or grid) =<br>
ns_type = grid<br>
; Periodic boundary conditions: xyz or no =<br>
pbc
= xyz<br>
; nblist cut-off =<br>
rlist = 1.0<br>
domain-decomposition = no<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW =<br>
; Method for doing electrostatics =<br>
coulombtype
= PME ;Reaction-Field<br>
rcoulomb-switch = 0<br>
rcoulomb
= 1.0 ;2.0<br>
; Dielectric constant (DC) for cut-off or DC of reaction field =<br>
epsilon_r = 80.0<br>
epsilon_rf = 1<br>
;I have done some thing new according to mannual and warnings and error<br>
; Method for doing Van der Waals =<br>
vdwtype = Cut-off<br>
; cut-off lengths =<br>
rvdw-switch = 0<br>
rvdw
= 1.0<br>
; Apply long range dispersion corrections for Energy and Pressure =<br>
DispCorr = No<br>
; Spacing for the PME/PPPM FFT grid =<br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used =<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters =<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 3d<br>
epsilon_surface = 0<br>
optimize_fft = yes<br>
<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br>
; Temperature coupling =<br>
Tcoupl = berendsen<br>
; Groups to couple separately =<br>
tc-grps
= DPP SOL PRO<br>
; Time constant (ps) and reference temperature (K) =<br>
tau_t
= 0.1 0.1 0.1 <br>
ref_t
= 310 310 310 <br>
; Pressure coupling =<br>
Pcoupl = berendsen<br>
Pcoupltype = semiisotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br>
tau_p
= 1.0 1.0<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p
= 1.0 1.0<br>
<br>
; SIMULATED ANNEALING CONTROL =<br>
annealing = no<br>
; Time at which temperature should be zero (ps) =<br>
;zero-temp_time = 0<br>
;I have commute the above line as it has no exitance<br>
<br>
; GENERATE VELOCITIES FOR STARTUP RUN =<br>
gen_vel = yes<br>
gen_temp = 310.0<br>
gen_seed = 173529<br>
<br>
; OPTIONS FOR BONDS =<br>
constraints = all-bonds<br>
; Type of constraint algorithm =<br>
constraint_algorithm = lincs<br>
; Do not constrain the start configuration =<br>
continuation = yes<br>
;unconstrained-start = no<br>
; Use successive overrelaxation to reduce the number of shake iterations =<br>
Shake-SOR = no<br>
; Relative tolerance of shake =<br>
shake-tol = 0.0001<br>
; Highest order in the expansion of the constraint coupling matrix =<br>
lincs_order = 4<br>
; Lincs will write a warning to the stderr if in one step a bond =<br>
; rotates over more degrees than =<br>
lincs-warnangle = 30<br>
; Convert harmonic bonds to morse potentials =<br>
morse = no<br>
<br>
<br>
<br>
;COM pulling<br>
pull
= umbrella<br>
pull_geometry = cylinder<br>
pull_dim = N N Y<br>
pull_r1 = 1<br>
pull_r0 = 1<br>
;pull_constr_tot = 1e-6<br>
pull_start = yes<br>
pull_nstxout = 10<br>
pull_nstfout = 1<br>
pull_ngroups = 1<br>
;name of reference group<br>
pull_group0 = DPP<br>
;pull_weights = 0<br>
;name of pull group<br>
pull_group1 = PIP<br>
;pull_weights = 0<br>
pull_vec1 = 0.0 0.0 -1<br>
;ref. distance at t=0<br>
pull_init1 =<br>
;rate of change of ref. gr. [nm/ps]<br>
pull_rate1 = 0.0005<br>
;force constant [KJ mol^-1 nm^-2]<br>
pull_k1 = 500<br>
;pull_kB1 =<br>
<br>
<br>
<br>
; ENERGY GROUP EXCLUSIONS =<br>
; Pairs of energy groups for which all non-bonded interactions are excluded =<br>
energygrp_excl =<br>
<br>
; NMR refinement stuff =<br>
; Distance restraints type: No, Simple or Ensemble =<br>
disre = No<br>
; Force weighting of pairs in one distance restraint: Conservative or Equal =<br>
disre-weighting = Conservative<br>
; Use sqrt of the time averaged times the instantaneous violation =<br>
disre-mixed = no<br>
disre-fc = 1000<br>
disre-tau = 0<br>
; Output frequency for pair distances to energy file =<br>
nstdisreout = 100<br>
; Orientation restraints: No or Yes =<br>
orire = no<br>
; Orientation restraints force constant and tau for time averaging =<br>
orire-fc = 0<br>
orire-tau = 0<br>
orire-fitgrp =<br>
; Output frequency for trace(SD) to energy file =<br>
nstorireout = 100<br>
<br>
; Free energy control stuff =<br>
free-energy = no<br>
init-lambda = 0<br>
delta-lambda = 0<br>
sc-alpha = 0<br>
sc-sigma = 0.3<br>
<br>
; Non-equilibrium MD stuff =<br>
acc-grps =<br>
accelerate =<br>
freezegrps =<br>
freezedim =<br>
cos-acceleration = 0<br>
<br>
; Electric fields =<br>
; Format is number of terms (int) and for all terms an amplitude (real) =<br>
; and a phase angle (real) =<br>
E-x
=<br>
E-xt =<br>
E-y
=<br>
E-yt =<br>
E-z
=<br>
E-zt =<br>
<br>
; User defined thingies =<br>
user1-grps =<br>
user2-grps =<br>
userint1 = 0<br>
userint2 = 0<br>
userint3 = 0<br>
userint4 = 0<br>
userreal1 = 0<br>
userreal2 = 0<br>
userreal3 = 0<br>
userreal4 = 0<br>
<br>