[gmx-users] protein in water production run

[sudheer babu]

Hi gmx users,
I am doing Protein in water prodcution run , my system is fine till 500ps
run, after that when I gave another 250 ps run, job was stopped and shown
following error

Step 28019, time 56.038 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000017 (between atoms 203 and 204) rms 0.000002
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

t = 56.038 ps: Water molecule starting at atom 20857 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Large VCM(group rest):     -1.84782,     -1.78497,     -1.69071, ekin-cm:
5.76677e+05

Step 28020  Warning: pressure scaling more than 1%, mu: 1.35376 1.35376
1.35376

Step 28020, time 56.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1.486033 (between atoms 56 and 57) rms 0.204923
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      3   90.0    0.1000   0.1297      0.1000
      9     10   64.9    0.1000   0.1000      0.1000
     17     18   31.4    0.1000   0.1000      0.1000
     22     23   51.4    0.1000   0.1000      0.1000
     29     30   30.5    0.1000   0.1000      0.1000
     41     42   90.0    0.1000   0.1104      0.1000
     47     48   30.6    0.1000   0.1015      0.1000
     47     49   90.0    0.1000   0.1448      0.1000
     52     53   81.1    0.1000   0.1000      0.1000
     56     57   90.0    0.1000   0.2486      0.1000
     61     62   90.0    0.1000   0.1019      0.1000
     90     91   90.0    0.1000   0.1019      0.1000
    446    447   33.8    0.1080   0.1080      0.1080
    448    449   50.3    0.1080   0.1080      0.1080
    452    453   38.6    0.1080   0.1080      0.1080
    454    455   90.0    0.1080   0.1546      0.1080
    470    471   90.0    0.1000   0.1070      0.1000
    478    479   90.0    0.1000   0.1894      0.1000
    486    487   35.9    0.1000   0.1000      0.1000
    491    492   90.0    0.1000   0.1350      0.1000
    498    499   31.7    0.1000   0.1000      0.1000
    509    510   83.7    0.1000   0.1000      0.1000
    535    536   90.0    0.1000   0.1610      0.1000
    541    542   75.4    0.1000   0.1030      0.1000
    541    543   90.0    0.1000   0.1890      0.1000
Constraint error in algorithm Lincs at step 28020
t = 56.040 ps: Water molecule starting at atom 20800 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Large VCM(group Protein):     -0.02381,     -0.00400,     -0.02590,
ekin-cm:  4.04275e+00
Large VCM(group rest): -679173760.00000, -911115136.00000, 14881016.00000,
ekin-cm:  7.87449e+22Large VCM(group Protein):     -0.02381,     -0.00400,
-0.02590, ekin-cm:  4.04275e+00
Large VCM(group rest): -679173760.00000, -911115136.00000, 14881016.00000,
ekin-cm:  7.87449e+22

 I am pasting my md.mdp file

title               =  dpt_prod
constraints         =  hbonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  125000   ; total 250 ps.
nstcomm             =  1
nstxout             =  100
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.4
pbc                 =  xyz
comm_grps           =  Protein
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein   SOL_Na
tau_t               =  0.1       0.1
ref_t               =  300       300
; isotropic pressure coupling is now on
Pcoupl              =  Berendsen
pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Energy monitoring
energygrps          =  Protein  SOL_Na
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300
gen_seed            =  173529

Pls help me ,

Thanks in advance.......
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