Dear All<br>I am using this .mdp file and I recived the below warnings,I can't solve that.<br><br><br>title = NPT<br>define = <br>integrator = md<br>tinit = 0<br>
dt = 0.002<br>nsteps = 500000<br>nstcomm = 1<br>comm-grps = protein non-protein<br>niter = 20<br>nstxout = 5000<br>
nstvout = 5000<br>nstfout = 0<br>nstlog = 5000<br>nstenergy = 250<br>nstxtcout = 250<br>xtc-precision = 1000<br>xtc_grps = protein non-protein<br>
energygrps = Protein non-protein<br>nstlist = 5<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.4<br>domain-decomposition = no<br>coulombtype = PME<br>
rcoulomb-switch = 0<br>rcoulomb = 1.4<br>epsilon-r = 1<br>vdw-type = Cut-off<br>rvdw-switch = 0<br>rvdw = 1.4<br>DispCorr = EnerPres<br>
fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-05<br>epsilon_surface = 0<br>
optimize_fft = no<br>tcoupl = Nose-hoover<br>tc-grps = Protein non-protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>Pcoupl = Parrinello-Rahman<br>
Pcoupltype = Isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>annealing = no<br>gen_vel = yes<br>gen_temp = 310<br>
gen_seed = 173529<br>constraints = all-bonds<br>constraint-algorithm = Lincs<br>unconstrained-start = no<br>lincs-order = 4<br>lincs-warnangle = 30<br>morse = no<br>
<br>my sytem is protein-ligand,I want to generate a NPT.<br>the result was:<br><br>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.002537, max 0.119994 (between atoms 5293 and 5294)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>starting mdrun 'Protein in water'<br>500000 steps, 1000.0 ps.<br><br>Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 5264 5263 41.7 0.1143 0.1261 0.1140<br>
5293 5294 82.7 0.1221 2612.9744 0.1090<br> 5291 5293 77.2 0.1517 6082.6147 0.1390<br> 5291 5292 101.0 0.1117 1518.6106 0.1090<br> 5289 5291 87.7 0.1353 6891.8911 0.1390<br>
5289 5290 88.4 0.1437 7529.4878 0.1360<br> 5289 5287 88.4 0.1456 7540.4873 0.1390<br> 5287 5288 89.7 0.1092 381.5114 0.1090<br> 5285 5287 92.3 0.1395 354.9220 0.1390<br>
5285 5286 123.8 0.1101 44.8448 0.1090<br> 5284 5293 89.0 0.1478 4605.1763 0.1390<br> 5284 5285 79.3 0.1402 173.5627 0.1390<br> 5278 5279 78.9 0.1529 1.1270 0.1530<br>
5277 5278 122.9 0.1545 13.1423 0.1530<br> 5276 5284 84.9 0.1422 159.0098 0.1390<br> 5276 5277 68.4 0.1543 90.8248 0.1530<br> 5276 5275 39.5 0.1439 72.5216 0.1430<br>
5274 5275 103.7 0.1436 21.6028 0.1430<br> 5273 5274 108.5 0.1394 3.3421 0.1390<br> 5276 5272 45.7 0.1402 80.6795 0.1390<br> 5272 5273 127.3 0.1340 14.2401 0.1330<br>
5272 5270 69.8 0.1336 12.6250 0.1330<br> 5270 5271 113.3 0.1092 0.2530 0.1090<br> 5268 5270 104.6 0.1391 0.2718 0.1390<br> 5268 5269 44.4 0.1091 0.1636 0.1090<br>
5273 5266 58.5 0.1342 14.0125 0.1330<br> 5265 5268 36.5 0.1394 0.1769 0.1390<br><br>Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#<br><br>Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#<br>
Wrote pdb files with previous and current coordinates<br>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<br>These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>Please let me know the solution.<br>Thanks in advance<br><br>
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