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在gromsacs里加电场后就mdrun不起来了 已有1人参与
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做的是dmf的模拟里面放有1mol nacl ，下面附上我的md.mdp信息，求大神帮助！！ title = OPLS Lysozyme MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 250000 dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 2 ps nstvout = 500 ; save velocities every 2 ps nstxtcout = 500 ; xtc compressed trajectory output every 2 ps nstenergy = 500 ; save energies every 2 ps nstlog = 500 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all_bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.8 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm) rvdw = 0.8 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = Ewald ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = MOL SOL NA CL ; two coupling groups - more accurate tau_t = 0.2 0.2 0.2 0.2 ; time constant, in ps ref_t = 298 298 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off nh-chain-length = 1 E-x = 1 3e5 0 出现的错误是 step 0: Water molecule starting at atom 619 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b.pdb to ./#step0b.pdb.4# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4# Wrote pdb files with previous and current coordinates step 0 WARNING: Listed nonbonded interaction between particles 6 and 2 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. step 1: Water molecule starting at atom 478 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1# Wrote pdb files with previous and current coordinates 段错误 (核心已转储) |
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小木虫: 金币+0.5, 给个红包，谢谢回帖
小木虫: 金币+0.5, 给个红包，谢谢回帖
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我也遇见同意的问题了，请问您解决了，怎么解决的 我还遇见，做npt的时候遇见的，nvt，em都没问题啊 WARNING: Listed nonbonded interaction between particles 1 and 13 at distance 2.504 which is larger than the table limit 2.016 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. step 0Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={-8.19631e-01, 0.00000e+00, 0.00000e+00} Box[ 1]={-0.00000e+00, -8.19631e-01, -0.00000e+00} Box[ 2]={-0.00000e+00, -0.00000e+00, -8.19631e-01} Can not fix pbc. Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={-8.19631e-01, 0.00000e+00, 0.00000e+00} Box[ 1]={-0.00000e+00, -8.19631e-01, -0.00000e+00} Box[ 2]={-0.00000e+00, -0.00000e+00, -8.19631e-01} Can not fix pbc. 段错误 (核心已转储) |
2楼2015-09-04 16:21:53