[gmx-users] Error in equilibration

[s lal badshah]

Dear Justin & Mark,
Hi! 
I made changes in my pr.mdp file but still the errors came.Please guide me.
title           = pr.mdp
cpp             = /usr/bin/cpp
define          = -DPOSRES
constraints     = all-bonds
integrator      = md
dt              = 0.002
nsteps          = 100000
nstcomm         = 1
nstxout         = 250
nstvout         = 1000
nstlog          = 10
nstenergy       = 10
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
vdwtype         = cut-off
rvdw            = 1.4
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e5
optimize_fft    = yes
;Berendsen temperature coupling is on
Tcoupl          = berendsen
tau_t           = 0.1       0.1 
tc-grps          = protein  non-protein
ref_t           = 298       298 
;Pressure coupling is on
Pcoupl          = berendsen
tau_p           = 20
compressibility = 4.5e-5
ref_p           = 1.0
;Generate velocities is on at 298 K
gen_vel         = yes
gen_temp        = 298
gen_seed        = 173529



Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 224.227219 (between atoms 1932 and 1934) rms 4.182889
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    198    200   49.7    0.1449   0.1615      0.1449
    200    201   90.1    0.1090   1.2644      0.1090
    200    202   46.8    0.1529   0.1690      0.1529
    200    211   41.2    0.1522   0.1686      0.1522
    264    265   70.9    0.1229   0.1349      0.1229
    264    266   47.2    0.1335   0.1443      0.1335
    266    267   67.0    0.1010   0.1148      0.1010
----------------------------------------------------------------------------------
step 0Warning: 1-4 interaction between 196 and 201 at distance 1.104 which is larger than the 1-4 table size 1.000 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

Step 1  Warning: pressure scaling more than 1%, mu: -6.71376e+08 -6.71376e+08 -6.71376e+08

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 10623.531250 (between atoms 1932 and 1933) rms 207.528702
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    170    172   63.2    0.1335   0.1515      0.1335
    172    173   41.5    0.1449   0.1423      0.1449
    172    181   87.7    0.1449   0.2689      0.1449
    173    174   38.5    0.1090   0.1402      0.1090
    173    184   33.3    0.1522   0.1855      0.1522
    175    178   64.7    0.1529   0.2016      0.1529
----------------------------------------------------------------------------------------
   2565   2576   59.4    0.1522   0.1316      0.1522
   2567   2568   38.4    0.1090   0.0818      0.1090
-------------------------------------------------------
Program mdrun, VERSION 3.3.1
Source code file: ns.c, line: 265

Fatal error:
Box was shifted at least 10 times. Please see log-file.
-------------------------------------------------------

Regards,
Lal badshah

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