[gmx-users] ERROR: Number of grid cells is zero
udaya kiran marelli
kiran.udaya at gmail.com
Mon Jul 11 21:29:23 CEST 2011
I am trying to do the NPT equilibration of a cyclic peptide in DMSO solvent
BOX using all atom charm force field (ffcharmm27) on GROMACS. The NVT
equilibration is working but the NPT equilibration shows the following
ERROR.
Back Off! I just backed up results/eq50K.log to results/#eq50K.log.1#
Reading file in1bar50K.tpr, VERSION 4.0.5 (double precision)
Back Off! I just backed up results/eq50K.trr to results/#eq50K.trr.1#
Back Off! I just backed up results/eq50K.xtc to results/#eq50K.xtc.1#
Back Off! I just backed up results/eq50K.edr to results/#eq50K.edr.1#
starting mdrun '16CHA in DMSO'
25000 steps, 50.0 ps.
[2] Done nedit eq.csh
Inner product between old and new vector <= 0.0!
constraint #45 atoms 44 and 46
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #45 atoms 44 and 46
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #48 atoms 46 and 52
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #34 atoms 34 and 35
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 26 and 36 at distance 153.333 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 632 Warning: pressure scaling more than 1%, mu: 190.046 190.046
190.046
Inner product between old and new vector <= 0.0!
constraint #39 atoms 38 and 39
Wrote pdb files with previous and current coordinates
Step 633 Warning: pressure scaling more than 1%, mu: 252.207 252.207
252.207
Inner product between old and new vector <= 0.0!
constraint #8 atoms 6 and 12
Wrote pdb files with previous and current coordinates
Step 634 Warning: pressure scaling more than 1%, mu: 1.23498 1.23498
1.23498
Inner product between old and new vector <= 0.0!
constraint #5 atoms 2 and 5
Wrote pdb files with previous and current coordinates
There were 2 inconsistent shifts. Check your topology
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
-------------------------------------------------------
Corresponding .mdp file is as follows.
;*-------------START_[7.3]-----------------------------------------------------------------------------------------
;*
;*-------------GENERAL_[7.3.1]-------------------------------------------------------------------------------------
;*
;* User
;*
;*
;*
;* COMMENTS:
;*
;*-------------PREPROCESSING_[7.3.2]-------------------------------------------------------------------------------
title = Free MD
cpp = /lib/cpp ; Vorprozessor
;include ; Einfuegen von
Topology-File-Verzeichnissen
;define = ; genaue Definition
des Top-Files, z.B. Restraints
;*
;*-------------RUN_CONTROL_[7.3.3]---------------------------------------------------------------------------------
integrator = md ; Algorithmus: steep empfolen
;tinit
dt = 0.002 ; [ZEIT: 0.001]
Integrationsschritte in ps !
nsteps = 250000 ; [SCHRITTE: 0] Summe aller
Integrationsschritte (aktuell: 10ps)
;init_step
comm_mode = linear
nstcomm = 500 ; [SCHRITTE: 1] Frequenz der
Massenzentrumsbewegung
comm_grps = system
;*
;*-------------LANGEVIN_DYNAMICS_[7.3.4]---------------------------------------------------------------------------
;bd_temp
;bd_fric
ld_seed =
;*
;*-------------ENERGY_MINIMIZATION_[7.3.5]-------------------------------------------------------------------------
;emtol = 100
;emstep = 0.01
;nstcgsteep = 50
;nbfgscorr = 10
;*
;*-------------SHELL_MOLECULAR_DYNAMICS_[7.3.6]--------------------------------------------------------------------
;emtol
;niter
;*
;*-------------OUTPUT_CONTROL_[7.3.7]------------------------------------------------------------------------------
nstxout = 50000 ; [SCHRITTE: 100] Frequenz des
Schreibens der Koordinaten
nstvout = 50000 ; [SCHRITTE: 100] Frequenz des
Schreibens der Geschwindigkeiten
nstfout = 50000 ; [SCHRITTE: 0] Frequenz des
Schreibens der Kraefte
nstlog = 50000 ; [SCHRITTE: 100] Frequenz des
Schreibens der Energien (in log-File)
nstenergy = 500 ; [SCHRITTE: 100] Frequenz
des Schreibens der Energien (in Energy-File)
nstxtcout = 500
xtc_precision = 1000
xtc_grps = 16CHA
energygrps = 16CHA DMSO
;*
;*-------------NEIGHBOUR_SEARCHING_[7.3.8]-------------------------------------------------------------------------
nstlist = 5 ; [SCHRITTE: 10] Frequenz des
Updates der Neighbour-List
ns_type = grid ; Neighbour-Listen-Typ
pbc = xyz
rlist = 0.8
;domain-decomposition = no
;*
;*-------------ELECTROSTATIC_&_VDW_[7.3.9]-------------------------------------------------------------------------
coulombtype = reaction-field
;rcoulomb_switch = 0.0
rcoulomb = 1.4
;epsilon_r = 1
epsilon_rf = 38
vdwtype = cut-off
;rvdw_switch = 0.0
rvdw = 1.4
;dispcorr =
;table-extension
;fourierspacing = 0.12
;(fourier_nx ;fourier_ny; fourier_nz)
;pme_order = 4
;ewald_rtol = 1e-06
;epsilon_surface = 0
;ewald_geometry
optimize_fft = yes
;*
;*--------------TEMPERATURE_COUPLING_[7.3.10]-----------------------------------------------------------------------
tcoupl = v-rescale
tc_grps = system
tau_t = 0.1
ref_t = 50
;*
;*--------------PRESSURE_COUPLING_[7.3.11]--------------------------------------------------------------------------
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 2.0
compressibility = 5.22e-05 ; DMSO isothermal compressibility
(for Water: 4.50e-05 bar-1)
ref_p = 1.0
;*
;*---------------SIMULATED_ANNEALING_[7.3.12]-----------------------------------------------------------------------
;annealing
;annealing_npoints
;annealing_time
;annealing_temp
;*
;*---------------VELOCITY_
GENERATION_[7.3.13]----------------------------------------------------------------------
gen_vel = no
gen_temp = 50
gen_seed = 173529
;*
;*---------------BONDS_[7.3.14]-------------------------------------------------------------------------------------
constraints = all-bonds
constraint_algorithm = shake
continuation = yes
shake_tol = 0.0001
;lincs_order = 4
;lincs_iter = 1
;lincs_warnangle = 30
;morse
;*
;*---------------ENERGY_GROUP_EXCLUSIONS_[7.3.15]-------------------------------------------------------------------
;energygrp_excl =
;*
;*---------------NMR_REFINEMENT_[7.3.16]----------------------------------------------------------------------------
;disre
;disre_weighting
;disre_mixed
;disre_fc
;disre_tau
;nstdisreout
;orire
;orire_fc
;orire_tau
;orire_fitgrp
;nstorireout
;dihre
;dihre_fc
;dihre_tau
;nstdihreout
;*
;*---------------FREE_ENERGY_PERTURBATION_[7.3.17]------------------------------------------------------------------
;free_energy =
;init_lambda =
;delta_lambda =
;sc_alpha =
;sc_power =
;sc_sigma =
;*
;*---------------NON-EQUILIBRIUM_MD_[7.3.18]------------------------------------------------------------------------
;acc_grps
;accelerate
;freezegrps =
;freezedim =
;cos_acceleration
;*
;*---------------ELECTRIC_FIELDS_[7.3.19]---------------------------------------------------------------------------
;(E_x; E_y; E_z)
;(E_xt; E_yt; E_zt)
;*
;*---------------USER_DEFINED_THINGIES_[7.3.20]---------------------------------------------------------------------
;(user1_grps; user2_grps)
;(userint1; userint2; userint3; userint4)
;(userreal1; userreal2; userreal3; userreal4)
;*
;*---------------END_[7.3]------------------------------------------------------------------------------------------
I had a look on the archives list already and implemented the earlier
suggested remarks but still the problem persists.
Could you please suggest what could be the problem?
Regards,
Uday.
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