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来围观啊新虫 (小有名气)
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[求助]
GROMCS出现错误
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求助各位大佬，在用gromacs的时候出现了以下的错误该如何解决呢？体系已经做了能量优化，这个错误是在做nvt预平衡的时候出现的。谢谢各位大佬！！ Step 1325, time 1.325 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035172, max 0.281169 (between atoms 142 and 145) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 143 144 31.2 0.1005 0.0989 0.1000 Step 1331, time 1.331 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 816.149048, max 9026.031250 (between atoms 143 and 144) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 103 127 48.7 0.1453 0.1471 0.1435 114 115 49.4 0.1566 0.0854 0.1435 114 124 98.6 0.1649 0.1101 0.1520 117 118 38.8 0.1835 0.3072 0.1520 117 141 106.8 0.1585 0.1745 0.1435 118 119 45.0 0.1661 0.0786 0.1435 118 126 67.7 0.1792 0.0449 0.1520 119 120 37.4 0.1027 0.1192 0.1000 121 124 35.8 0.1524 0.2155 0.1520 124 125 38.1 0.1444 0.1945 0.1435 125 126 30.7 0.1466 0.1670 0.1435 128 129 176.2 0.2776 5.3298 0.1435 128 131 69.7 0.5636 4.4779 0.1520 128 138 79.8 0.3747 3.8723 0.1520 129 130 93.1 0.0182 2.2967 0.1000 131 132 56.9 0.3678 1.8625 0.1520 131 155 118.5 1.1285 4.6649 0.1435 132 133 105.0 0.1806 15.4852 0.1435 132 140 48.7 0.0869 0.9637 0.1520 133 134 98.4 0.1397 15.0138 0.1000 135 136 87.5 0.1530 1.4493 0.1435 135 138 82.6 0.1740 2.9280 0.1520 136 137 92.0 0.1226 0.7336 0.1000 138 139 177.3 0.1450 16.4410 0.1435 139 140 59.1 0.1621 16.2713 0.1435 140 141 95.8 0.1300 0.8640 0.1435 142 145 99.8 4.3105 38.1381 0.1520 142 152 149.1 4.6295 6.3105 0.1520 145 146 31.5 2.1491 40.9124 0.1520 145 171 49.5 2.5563 41.1024 0.1435 146 147 93.5 3.6932 3.2399 0.1435 146 154 33.9 2.4452 7.8218 0.1520 147 148 89.6 1.6534 1.7318 0.1000 149 150 92.5 0.8919 0.8930 0.1435 149 152 86.2 4.6661 10.1095 0.1520 150 151 92.4 0.4329 1.0297 0.1000 152 153 64.5 5.4649 13.5725 0.1435 153 154 156.7 4.2225 6.0705 0.1435 154 155 31.8 3.5694 6.1695 0.1435 157 158 127.9 0.1700 0.2188 0.1000 159 162 34.4 0.7675 1.7566 0.1520 160 161 58.5 0.3207 0.2597 0.1000 162 163 62.7 0.5360 0.5178 0.1435 162 170 84.9 2.2265 4.8269 0.1520 163 164 74.8 0.6339 0.2147 0.1000 166 167 55.6 0.1750 0.0975 0.1000 168 169 69.1 0.4028 1.2414 0.1435 169 170 85.7 2.0814 3.6421 0.1435 170 171 124.3 1.6610 4.1818 0.1435 170 171 124.3 1.6610 4.1818 0.1435 170 171 124.3 1.6610 4.1818 0.1435 step 1331: Water molecule starting at atom 4837 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1331b.pdb to ./#step1331b.pdb.1# Back Off! I just backed up step1331c.pdb to ./#step1331c.pdb.1# Wrote pdb files with previous and current coordinates 段错误 ******************************************************************************************************************************************** 以下为minim.mdp的参数 ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.4 ; Short-range electrostatic cut-off rvdw = 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ******************************************************************************************************************************************* 以下为nvt restraint的预平衡参数nvt.mdp： define = -DPOSRES ; position restrain the protein integrator = sd dt = 0.001 ; ps nsteps =100000 ; = tot nstcomm = 10000 nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 10000 nstenergy = 1000 nstlist = 5 pbc = xyz ns_type = grid coulombtype = PME rcoulomb = 1.2 pme_order = 5 ; cubic interpolation fourierspacing = 0.175 ; grid spacing for FFT vdwtype = cut-off rvdw = 1.2 rlist = 1.2 DispCorr = EnerPres ;optimize_fft = yes ;epsilon_r = 80 ;Couplig Temp tcoupl = v-rescale tau_t = 0.2 tc-grps = System ref_t = 298 ;Costrain Bond constraints = all-bonds constraint_algorithm = LINCS ;Coupling P ;Pcoupl = berendsen ;Pcoupltype = isotropic ;tau_p = 0.5 ;compressibility = 4.5e-5 ;ref_p=1 ;Generate velocity gen_vel = yes gen_temp = 298.0 gen_seed = 333529@smutao@smutao@oxox6085@oxox6085 |
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