Dear Justin & Mark, Hi! I made changes in my pr.mdp file but still the errors came.Please guide me. title = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 100000 nstcomm = 1 nstxout = 250 nstvout = 1000 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e5 optimize_fft = yes ;Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 298 298 ;Pressure coupling is on Pcoupl = berendsen tau_p = 20 compressibility = 4.5e-5 ref_p = 1.0 ;Generate velocities is on at 298 K gen_vel = yes gen_temp = 298 gen_seed = 173529
Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 224.227219 (between atoms 1932 and 1934) rms 4.182889 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 198 200 49.7 0.1449 0.1615 0.1449 200 201 90.1 0.1090 1.2644 0.1090 200 202 46.8 0.1529 0.1690 0.1529 200 211 41.2 0.1522 0.1686 0.1522 264 265 70.9 0.1229 0.1349 0.1229 264 266 47.2 0.1335 0.1443 0.1335 266 267 67.0 0.1010 0.1148 0.1010 ---------------------------------------------------------------------------------- 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 These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 1 Warning: pressure scaling more than 1%, mu: -6.71376e+08 -6.71376e+08 -6.71376e+08 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 10623.531250 (between atoms 1932 and 1933) rms 207.528702 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 170 172 63.2 0.1335 0.1515 0.1335 172 173 41.5 0.1449 0.1423 0.1449 172 181 87.7 0.1449 0.2689 0.1449 173 174 38.5 0.1090 0.1402 0.1090 173 184 33.3 0.1522 0.1855 0.1522 175 178 64.7 0.1529 0.2016 0.1529 ---------------------------------------------------------------------------------------- 2565 2576 59.4 0.1522 0.1316 0.1522 2567 2568 38.4 0.1090 0.0818 0.1090 ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: ns.c, line: 265 Fatal error: Box was shifted at least 10 times. Please see log-file. ------------------------------------------------------- Regards, Lal badshah Send instant messages to your online friends http://uk.messenger.yahoo.com
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