Dear Justin & Mark,<br>Hi! <br>I made changes in my pr.mdp file but still the errors came.Please guide me.<br>title = pr.mdp<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002<br>nsteps = 100000<br>nstcomm = 1<br>nstxout = 250<br>nstvout = 1000<br>nstlog = 10<br>nstenergy =
10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e5<br>optimize_fft = yes<br>;Berendsen temperature coupling is on<br>Tcoupl = berendsen<br>tau_t =
0.1 0.1 <br>tc-grps = protein non-protein<br>ref_t = 298 298 <br>;Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 20<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>;Generate velocities is on at 298 K<br>gen_vel = yes<br>gen_temp = 298<br>gen_seed = 173529<br><br><br><br>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max 224.227219 (between atoms 1932 and 1934) rms 4.182889<br>bonds that rotated more than 30 degrees:<br> atom 1
atom 2 angle previous, current, constraint length<br> 198 200 49.7 0.1449 0.1615 0.1449<br> 200 201 90.1 0.1090 1.2644 0.1090<br> 200 202 46.8 0.1529 0.1690 0.1529<br> 200 211 41.2 0.1522 0.1686 0.1522<br> 264 265 70.9 0.1229 0.1349 0.1229<br> 264 266 47.2 0.1335 0.1443 0.1335<br> 266
267 67.0 0.1010 0.1148 0.1010<br>----------------------------------------------------------------------------------<br>step 0Warning: 1-4 interaction between 196 and 201 at distance 1.104 which is larger than the 1-4 table size 1.000 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><br>Step 1 Warning: pressure scaling more than 1%, mu: -6.71376e+08 -6.71376e+08 -6.71376e+08<br><br>Step 1, time 0.002 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max 10623.531250 (between atoms 1932 and 1933) rms 207.528702<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 170 172 63.2 0.1335
0.1515 0.1335<br> 172 173 41.5 0.1449 0.1423 0.1449<br> 172 181 87.7 0.1449 0.2689 0.1449<br> 173 174 38.5 0.1090 0.1402 0.1090<br> 173 184 33.3 0.1522 0.1855 0.1522<br> 175 178 64.7 0.1529 0.2016 0.1529<br>----------------------------------------------------------------------------------------<br> 2565 2576 59.4 0.1522
0.1316 0.1522<br> 2567 2568 38.4 0.1090 0.0818 0.1090<br>-------------------------------------------------------<br>Program mdrun, VERSION 3.3.1<br>Source code file: ns.c, line: 265<br><br>Fatal error:<br>Box was shifted at least 10 times. Please see log-file.<br>-------------------------------------------------------<br><br>Regards,<br>Lal badshah<br><p> Send instant messages to your online friends http://uk.messenger.yahoo.com