[gmx-users] so difficult problem

[mohsen ramezanpour]

Dear All
I am using this .mdp file and I recived the below warnings,I can't solve
that.


title                    = NPT
define                   =
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 500000
nstcomm                  = 1
comm-grps                = protein non-protein
niter                    = 20
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
nstlog                   = 5000
nstenergy                = 250
nstxtcout                = 250
xtc-precision            = 1000
xtc_grps                 = protein non-protein
energygrps               = Protein  non-protein
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.4
domain-decomposition     = no
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.4
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.4
DispCorr                 = EnerPres
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no
tcoupl                   = Nose-hoover
tc-grps                  = Protein     non-protein
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
annealing                = no
gen_vel                  = yes
gen_temp                 = 310
gen_seed                 = 173529
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = no
lincs-order              = 4
lincs-warnangle          = 30
morse                    = no

my sytem is protein-ligand,I want to generate a NPT.
the result was:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'Protein in water'
500000 steps,   1000.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5264   5263   41.7    0.1143   0.1261      0.1140
   5293   5294   82.7    0.1221 2612.9744      0.1090
   5291   5293   77.2    0.1517 6082.6147      0.1390
   5291   5292  101.0    0.1117 1518.6106      0.1090
   5289   5291   87.7    0.1353 6891.8911      0.1390
   5289   5290   88.4    0.1437 7529.4878      0.1360
   5289   5287   88.4    0.1456 7540.4873      0.1390
   5287   5288   89.7    0.1092 381.5114      0.1090
   5285   5287   92.3    0.1395 354.9220      0.1390
   5285   5286  123.8    0.1101  44.8448      0.1090
   5284   5293   89.0    0.1478 4605.1763      0.1390
   5284   5285   79.3    0.1402 173.5627      0.1390
   5278   5279   78.9    0.1529   1.1270      0.1530
   5277   5278  122.9    0.1545  13.1423      0.1530
   5276   5284   84.9    0.1422 159.0098      0.1390
   5276   5277   68.4    0.1543  90.8248      0.1530
   5276   5275   39.5    0.1439  72.5216      0.1430
   5274   5275  103.7    0.1436  21.6028      0.1430
   5273   5274  108.5    0.1394   3.3421      0.1390
   5276   5272   45.7    0.1402  80.6795      0.1390
   5272   5273  127.3    0.1340  14.2401      0.1330
   5272   5270   69.8    0.1336  12.6250      0.1330
   5270   5271  113.3    0.1092   0.2530      0.1090
   5268   5270  104.6    0.1391   0.2718      0.1390
   5268   5269   44.4    0.1091   0.1636      0.1090
   5273   5266   58.5    0.1342  14.0125      0.1330
   5265   5268   36.5    0.1394   0.1769      0.1390

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965
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

Please let me know the solution.
Thanks in advance
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