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469187892银虫 (小有名气)
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[求助]
gromacs 运行npt时出错
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Fatal error: Too many LINCS warnings (2290) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1 but normally it is better to fix the problem 输入文件是 title = NPT Equilibration for KALP15-DPPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters freezegrps = HEM_2FE_4FE_3FE_r_57_r_62_r_77_r_65_r_150_r_153_r_217_r_156_r_213_r_160_r_207_r_335_r_442 freezedim = Y Y Y continuation = yes ; Restarting after NVT 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 cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics nhchainlength =1 coulombtype = PME ; 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 ; More accurate thermostat tc-grps = Protein_HEM_MOL_2FE_4FE_3FE DPPC SOL_CL ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 50 50 50 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 10.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, 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 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcalcenergy = 1 comm-mode = Linear comm-grps = Protein_HEM_MOL_2FE_4FE_3FE_DPPC SOL_CL ; Scale COM of reference coordinates refcoord_scaling = com 能帮忙找找错误吗？是参数设置的不合理，还是结构没有优化好? 我从网上下载的DPPC膜，http://moose.bio.ucalgary.ca/ind ... ures_and_Topologies， 还需要做npt, 和md 优化吗？ 大家做膜蛋白是先做nvt,还是npt? 问题有点多  |
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2楼2012-12-12 10:59:01
