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[求助]
gromacs做全原子模拟时候，突然到MD这一步出错
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 MD的控制文件是这样的：title = MD simulation ;Preprocessor cpp = /lib/cpp ;Directories to include in the topology format include = -I../top ;Run control: A leap-frog algorithm for integrating Newton's equations. integrator = md ;Total simulation time: 1000 ps :time step in femtoseconds dt = 0.002 ;number of steps nsteps = 10000000 ;frequency to write coordinates to output trajectory file nstxout = 5000 ;frequency to write velocities to output trajectory file nstvout = 5000 ;frequency to write energies to log file nstlog = 1000 ;frequency to write energies to energy file nstenergy = 1000 ;frequency to write coordinates to xtc trajectory nstxtcout = 1000 ;group(s) to write to xtc trajectory xtc_grps = OCT ;group(s) to write to energy file energygrps = OCT ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 5 ;Make a grid in the box and only check atoms in neighboring grid cells ;when constructing a new neighbor list every nstlist steps. ns_type = grid ;cut-off distance for the short-range neighbor list rlist = 1.0 ;treatment of electrostatic interactions coulombtype = PME rcoulomb = 1.0 fourierspacing =0.12 pme_order =4 ewald_rtol =1e-5 optimize_fft =yes ;treatment of van der waals interactions rvdw = 1.4 ; Periodic boudary conditions in all the directions pbc = xyz ;Temperature coupling tcoupl = berendsen tc-grps = OCT tau_t = 0.1 ref_t = 290 ;Pressure coupling ;Pcoupl = berendsen ;Pcoupltype = isotropic ;tau_p = 1.0 ;compressibility = 4.5e-5 ;ref_p = 1.0 ;Velocity generation gen_vel = yes gen_temp = 290 gen_seed = 173529 ; Type of constraint algorithm constraint-algorithm = Lincs lincs-iter = 4 ;Constrain bonds constraints = none 出现的错误是： creating statusfile for 1 node... ' for variable integrator, using 'md' Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi' ' for variable ns-type, using 'Grid' Next time use one of: 'Grid' 'Simple' ' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'full' ' for variable coulombtype, using 'Cut-off' Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User' ' for variable optimize_fft, using 'no' Next time use one of: 'no' 'yes' ' for variable tcoupl, using 'No' Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 'Andersen-interval' ' for variable gen-vel, using 'no' Next time use one of: 'no' 'yes' ' for variable constraints, using 'none' Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles' ' for variable constraint-algorithm, using 'Lincs' Next time use one of: 'Lincs' 'Shake' Fatal error: number of coordinates in coordinate file (box.pdb, 3900) does not match topology (octanebox.top, 0) top文件在能量最小化的那一步没有任何问题，但是在MD这一步就不行了。 |
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5楼2012-12-06 22:47:30
2楼2011-04-19 07:14:17
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; ; File 'octanebox.top' was generated ; By user: public (501) ; On host: cluster.hpc.org ; At date: Thu Apr 14 17:21:22 2011 ; ; This is your topology file ; PRODRG COORDS ; ; Include forcefield parameters #include "ffoplsaa.itp" ;include needed parameters #include "octane.itp" ; Include surfacetant topology #include "sds.itp" ;include water parameters #include "spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name octane box [ molecules ] ; Compound #mols OCT 150 |
3楼2011-04-19 13:56:05
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; ; .itp file for octane in OPLS force field ; Generated by HYF ; ; [ moleculetype ] ; Name nrexcl OCT 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_135 1 OCT C 1 -0.18 12.011 2 opls_140 1 OCT H 1 0.06 1.008 3 opls_140 1 OCT H 1 0.06 1.008 4 opls_140 1 OCT H 1 0.06 1.008 5 opls_136 1 OCT C 2 -0.12 12.011 6 opls_140 1 OCT H 2 0.06 1.008 7 opls_140 1 OCT H 2 0.06 1.008 8 opls_136 1 OCT C 3 -0.12 12.011 9 opls_140 1 OCT H 3 0.06 1.008 10 opls_140 1 OCT H 3 0.06 1.008 11 opls_136 1 OCT C 4 -0.12 12.011 12 opls_140 1 OCT H 4 0.06 1.008 13 opls_140 1 OCT H 4 0.06 1.008 14 opls_136 1 OCT C 5 -0.12 12.011 15 opls_140 1 OCT H 5 0.06 1.008 16 opls_140 1 OCT H 5 0.06 1.008 17 opls_136 1 OCT C 6 -0.12 12.011 18 opls_140 1 OCT H 6 0.06 1.008 19 opls_140 1 OCT H 6 0.06 1.008 20 opls_136 1 OCT C 7 -0.12 12.011 21 opls_140 1 OCT H 7 0.06 1.008 22 opls_140 1 OCT H 7 0.06 1.008 23 opls_135 1 OCT C 8 -0.18 12.011 24 opls_140 1 OCT H 8 0.06 1.008 25 opls_140 1 OCT H 8 0.06 1.008 26 opls_140 1 OCT H 8 0.06 1.008 [ bonds ] ; ai aj fu c0, c1, ... 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 8 1 8 9 1 8 10 1 8 11 1 11 12 1 11 13 1 11 14 1 14 15 1 14 16 1 14 17 1 17 18 1 17 19 1 17 20 1 20 21 1 20 22 1 20 23 1 23 24 1 23 25 1 23 26 1 [ pairs ] ; ai aj fu c0, c1, ... 2 6 1 2 7 1 2 8 1 3 6 1 3 7 1 3 8 1 4 6 1 4 7 1 4 8 1 1 9 1 1 10 1 1 11 1 6 9 1 6 10 1 6 11 1 7 9 1 7 10 1 7 11 1 5 12 1 5 13 1 5 14 1 9 12 1 9 13 1 9 14 1 10 12 1 10 13 1 10 14 1 8 15 1 8 16 1 8 17 1 12 15 1 12 16 1 12 17 1 13 15 1 13 16 1 13 17 1 11 18 1 11 19 1 11 20 1 15 18 1 15 19 1 15 20 1 16 18 1 16 19 1 16 20 1 14 21 1 14 22 1 14 23 1 18 21 1 18 22 1 18 23 1 19 21 1 19 22 1 19 23 1 17 24 1 17 25 1 17 26 1 21 24 1 21 25 1 21 26 1 22 24 1 22 25 1 22 26 1 [ angles ] ; ai aj ak fu c0, c1, ... 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 1 5 6 1 1 5 7 1 1 5 8 1 6 5 7 1 6 5 8 1 7 5 8 1 5 8 9 1 5 8 10 1 5 8 11 1 9 8 10 1 9 8 11 1 10 8 11 1 8 11 12 1 8 11 13 1 8 11 14 1 12 11 13 1 12 11 14 1 13 11 14 1 11 14 15 1 11 14 16 1 11 14 17 1 15 14 16 1 15 14 17 1 16 14 17 1 14 17 18 1 14 17 19 1 14 17 20 1 18 17 19 1 18 17 20 1 19 17 20 1 17 20 21 1 17 20 22 1 17 20 23 1 21 20 22 1 21 20 23 1 22 20 23 1 20 23 24 1 20 23 25 1 20 23 26 1 24 23 25 1 24 23 26 1 25 23 26 1 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 2 1 5 6 3 2 1 5 7 3 2 1 5 8 3 3 1 5 6 3 3 1 5 7 3 3 1 5 8 3 4 1 5 6 3 4 1 5 7 3 4 1 5 8 3 1 5 8 9 3 1 5 8 10 3 1 5 8 11 3 6 5 8 9 3 6 5 8 10 3 6 5 8 11 3 7 5 8 9 3 7 5 8 10 3 7 5 8 11 3 5 8 11 12 3 5 8 11 13 3 5 8 11 14 3 9 8 11 12 3 9 8 11 13 3 9 8 11 14 3 10 8 11 12 3 10 8 11 13 3 10 8 11 14 3 8 11 14 15 3 8 11 14 16 3 8 11 14 17 3 12 11 14 15 3 12 11 14 16 3 12 11 14 17 3 13 11 14 15 3 13 11 14 16 3 13 11 14 17 3 11 14 17 18 3 11 14 17 19 3 11 14 17 20 3 15 14 17 18 3 15 14 17 19 3 15 14 17 20 3 16 14 17 18 3 16 14 17 19 3 16 14 17 20 3 14 17 20 21 3 14 17 20 22 3 14 17 20 23 3 18 17 20 21 3 18 17 20 22 3 18 17 20 23 3 19 17 20 21 3 19 17 20 22 3 19 17 20 23 3 17 20 23 24 3 17 20 23 25 3 17 20 23 26 3 21 20 23 24 3 21 20 23 25 3 21 20 23 26 3 22 20 23 24 3 22 20 23 25 3 22 20 23 26 3 |
4楼2011-04-19 13:56:30
