Hi gmx users, <br>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<br><br>Step 28019, time 56.038 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>max 0.000017 (between atoms 203 and 204) rms 0.000002<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br><br>t = 56.038 ps: Water molecule starting at atom 20857 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates<br>Large VCM(group rest): -1.84782, -1.78497, -1.69071, ekin-cm: 5.76677e+05<br><br>Step 28020 Warning: pressure scaling more than 1%, mu: 1.35376 1.35376 1.35376<br>
<br>Step 28020, time 56.04 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max 1.486033 (between atoms 56 and 57) rms 0.204923<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
1 3 90.0 0.1000 0.1297 0.1000<br> 9 10 64.9 0.1000 0.1000 0.1000<br> 17 18 31.4 0.1000 0.1000 0.1000<br> 22 23 51.4 0.1000 0.1000 0.1000<br>
29 30 30.5 0.1000 0.1000 0.1000<br> 41 42 90.0 0.1000 0.1104 0.1000<br> 47 48 30.6 0.1000 0.1015 0.1000<br> 47 49 90.0 0.1000 0.1448 0.1000<br>
52 53 81.1 0.1000 0.1000 0.1000<br> 56 57 90.0 0.1000 0.2486 0.1000<br> 61 62 90.0 0.1000 0.1019 0.1000<br> 90 91 90.0 0.1000 0.1019 0.1000<br>
446 447 33.8 0.1080 0.1080 0.1080<br> 448 449 50.3 0.1080 0.1080 0.1080<br> 452 453 38.6 0.1080 0.1080 0.1080<br> 454 455 90.0 0.1080 0.1546 0.1080<br>
470 471 90.0 0.1000 0.1070 0.1000<br> 478 479 90.0 0.1000 0.1894 0.1000<br> 486 487 35.9 0.1000 0.1000 0.1000<br> 491 492 90.0 0.1000 0.1350 0.1000<br>
498 499 31.7 0.1000 0.1000 0.1000<br> 509 510 83.7 0.1000 0.1000 0.1000<br> 535 536 90.0 0.1000 0.1610 0.1000<br> 541 542 75.4 0.1000 0.1030 0.1000<br>
541 543 90.0 0.1000 0.1890 0.1000<br>Constraint error in algorithm Lincs at step 28020<br>t = 56.040 ps: Water molecule starting at atom 20800 can not be settled.<br>Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates<br>
Large VCM(group Protein): -0.02381, -0.00400, -0.02590, ekin-cm: 4.04275e+00<br>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<br>
Large VCM(group rest): -679173760.00000, -911115136.00000, 14881016.00000, ekin-cm: 7.87449e+22<br><br> I am pasting my md.mdp file <br><br>title = dpt_prod<br>constraints = hbonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 125000 ; total 250 ps.<br>nstcomm = 1<br>nstxout = 100<br>nstlog = 100<br>nstenergy = 100<br>nstlist = 10<br>
ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 1.4<br>pbc = xyz<br>comm_grps = Protein<br>; Berendsen temperature coupling is on in two groups<br>
Tcoupl = Berendsen<br>tc-grps = Protein SOL_Na<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>; isotropic pressure coupling is now on<br>Pcoupl = Berendsen<br>
pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Energy monitoring<br>energygrps = Protein SOL_Na<br>; Generate velocites is off at 300 K.<br>
gen_vel = no<br>gen_temp = 300<br>gen_seed = 173529<br><br>Pls help me , <br><br>Thanks in advance.......<br>