[gmx-users] protein in water production run

[David van der Spoel]

sudheer babu wrote:
> 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 !
time step is too long for hbond constraints. use 1 fs.
> 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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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se