[gmx-users] step 0Segmentation fault
ram bio
rmbio861 at gmail.com
Tue Oct 6 13:03:08 CEST 2009
Dear Justin,
Thanks for the advice. I am using the DPPC 128 lipid bilayer from D.
Peter Tieleman website, and the nvt.mdp file and the nvt.log files are
as follows as in your tutorial:
____________________________________________________________________________________________________________________________________________________________________________________
title = NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 323 323 323 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 323 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DPPC SOL_CL-
______________________________________
nvt.log file;
Input Parameters:
integrator = md
nsteps = 50000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 45
nky = 45
nkz = 42
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1.2
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 6048.01 12219 13680
ref_t: 323 323 323
tau_t: 0.1 0.1 0.1
anneal: No No No
ann_npoints: 0 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: 0.000
Generated table with 1100 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 2274 molecules.
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Removing pbc first time
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 9045
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: Protein_DPPC
1: SOL_CL-
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 15940 Atoms
Max number of connections per atom is 28
Total number of connections is 117957
Max number of graph edges per atom is 4
Total number of graph edges is 27186
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 9.42e-04
Initial temperature: 503.557 K
Started mdrun on node 0 Thu Jun 25 11:30:30 2009
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 9 x 9 cells
Large VCM(group Protein_DPPC): -50.08205, 97.99061,
16.32530, Temp-cm: 2.50669e+05
Long Range LJ corr.: <C6> 2.0307e-03
Long Range LJ corr.: Epot -1862.02, Pres: -184.12, Vir: 1862.02
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
1.48814e+04 8.19090e+03 8.43857e+03 6.38969e+03 2.93352e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.09831e+03 5.49186e+04 7.87055e+09 -1.86202e+03 -1.48414e+05
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-1.53985e+05 9.50084e+00 7.87034e+09 3.08099e+17 3.08099e+17
Conserved En. Temperature Pressure (bar) Cons. rmsd ()
3.08099e+17 2.31982e+15 1.01551e+16 7.25066e+04
Please diagnose the information and suggest.
Thanks
ram
On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Gromacs Users,
>>
>> I have inserted the protein in lipid bilayer and performed Inflategro
>> I am able to reach the required area per lipid after certain
>> iterations but was unable to get the standard Epot and Fmax values
>> that is negative and to the power of 5 or 6 and Fmax less than 1000
>
> You won't get that magnitude of Epot without water. If you can't reach Fmax
> < 1000, you shouldn't just plow ahead. Analyze where the problem is,
> because it is unlikely to go away by magic!
>
>> during the last minimization , later i solvated the protein using a
>> vanderwaal radii for carbon as 0.375, i found some water molecules not
>> in the core of the lipid layer but to the sides, as they were not in
>> the centre i ionated the complex with 13 chloride ions as the charge
>
> Did you get rid of these waters? You can always try tweaking the entry in
> vdwradii.dat for C. As far as those on the sides are concerned, it sounds
> like the box you've created is too large for the lipids. I wouldn't use
> this system, because you'll waste a huge amount of time hoping it
> equilibrates right.
>
>> shown was non-zero total intergral charge 1.30000e+01, then i minized
>> the ionized complex with the minim.mdp file in as per justin tutorial,
>> i am following all the mdp files as per the tutorial till now, and was
>> able to obtain Potential Energy = -1.8947278e+05
>> Maximum force = 9.1642163e+02 on atom 7647
>> Norm of force = 5.0845932e+01
>>
>
> That looks fine, but I still think there is an underlying problem in your
> InflateGRO construction step.
>
>> and then i created the index file ane while running the nvt
>> equilllibrqtion i am getting
>>
>> Step 0, time 0 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.007117, max 0.443345 (between atoms 6311 and 6312)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>>
>
> The classic case of "blowing up." See either my Advanced Troubleshooting
> page in the tutorial, or
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you want
> more specific advice, you'll have to provide information at least about what
> type of lipid you're using, and what you have in your .mdp file.
>
>> Can any body suggest me how to rectify the defect and is it the
>> problem with compliation as i am using gromacs 4.0.3 or the memory
>> space or my running the job.
>
> Well, first off I'd recommend always using the most current version of the
> software, not that it's likely to impact your system, but just in general.
> This is a problem reported to this list almost daily, so please also check
> the archives. There are literally thousands of posts regarding LINCS
> warnings and unstable systems.
>
> -Justin
>
>>
>> Thanks
>>
>> Ram
>> _______________________________________________
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>
> --
> ========================================
>
> 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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