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469187892銀蟲(chóng) (小有名氣)
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[求助]
gromacs 運(yùn)行npt時(shí)出錯(cuò)
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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 輸入文件是 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 能幫忙找找錯(cuò)誤嗎？是參數(shù)設(shè)置的不合理，還是結(jié)構(gòu)沒(méi)有優(yōu)化好? 我從網(wǎng)上下載的DPPC膜，http://moose.bio.ucalgary.ca/ind ... ures_and_Topologies， 還需要做npt, 和md 優(yōu)化嗎？ 大家做膜蛋白是先做nvt,還是npt? 問(wèn)題有點(diǎn)多  |
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【答案】應(yīng)助回帖
★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
zh1987hs: 金幣+3, 謝謝 2012-12-12 11:34:52
469187892: 金幣+10, ★★★很有幫助 2012-12-12 17:09:10
469187892: 金幣+10, ★★★很有幫助 2012-12-12 17:09:19
zh1987hs: 金幣+3, 謝謝 2012-12-12 11:34:52
469187892: 金幣+10, ★★★很有幫助 2012-12-12 17:09:10
469187892: 金幣+10, ★★★很有幫助 2012-12-12 17:09:19
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我曾經(jīng)做過(guò)類似的模擬： 1、em 2、nvt一小段兒 3、npt 到合理構(gòu)型 4、再長(zhǎng)時(shí)間NVT研究關(guān)注的計(jì)算 具體問(wèn)題具體分析，多看看新文獻(xiàn)吧 |
2樓2012-12-12 10:59:01
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