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[求助] gromacs软件中grompp命令运行出现警告已有1人参与

如题，我在运行《水中的溶菌酶》教程时，出现错误。不知道是什么原因，求大家解答

root@wu-MS-7788:~# grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
                     :-)  G  R  O  M  A  C  S  (-:

         Glycine aRginine prOline Methionine Alanine Cystine Serine

                        :-)  VERSION 4.6.5  (-:

      Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
         Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
   Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
      Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
         Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
            Michael Shirts, Alfons Sijbers, Peter Tieleman,

            Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
      Copyright (c) 2001-2012,2013, The GROMACS development team at
      Uppsala University & The Royal Institute of Technology, Sweden.
         check out http://www.gromacs.org for more information.

      This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
      as published by the Free Software Foundation; either version 2.1
         of the License, or (at your option) any later version.

                              :-)  grompp  (-:

Option    Filename  Type       Description
------------------------------------------------------------
  -f       md.mdp  Input       grompp input file with MD parameters
-po    mdout.mdp  Output    grompp input file with MD parameters
  -c       npt.gro  Input       Structure file: gro g96 pdb tpr etc.
  -r    conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
-rb    conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n    index.ndx  Input, Opt.  Index file
  -p    topol.top  Input       Topology file
-pp  processed.top  Output, Opt. Topology file
  -o    md_0_1.tpr  Output    Run input file: tpr tpb tpa
  -t       npt.cpt  Input, Opt!  Full precision trajectory: trr trj cpt
  -e    ener.edr  Input, Opt.  Energy file
-ref    rotref.trr  In/Out, Opt. Full precision trajectory: trr trj cpt

Option    Type Value Description
------------------------------------------------------
-[no]h    bool no    Print help info and quit
-[no]version bool no    Print version info and quit
-nice       int 0    Set the nicelevel
-[no]v    bool no    Be loud and noisy
-time       real -1    Take frame at or first after this time.
-[no]rmvsbds bool yes    Remove constant bonded interactions with virtual
                        sites
-maxwarn    int 0    Number of allowed warnings during input
                        processing. Not for normal use and may generate
                        unstable systems
-[no]zero bool no    Set parameters for bonded interactions without
                        defaults to zero instead of generating an error
-[no]renum bool yes    Renumber atomtypes and minimize number of
                        atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#

WARNING 1 [file md.mdp, line 47]:
  Unknown left-hand 'nstxout-compressed' in parameter file

WARNING 2 [file md.mdp, line 47]:
  Unknown left-hand 'compressed-x-grps' in parameter file

Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 129 Protein residues
There are: 10824    Water residues
There are:    8       Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group Protein is 3895.83
Number of degrees of freedom in T-Coupling group non-Protein is 64965.17
Determining Verlet buffer for an energy drift of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.035 nm, buffer size 0.035 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame       -1 time  100.000
Using frame at t = 100 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 44x44x44, spacing 0.159 0.159 0.159
Estimate for the relative computational load of the PME mesh part: 0.16
This run will generate roughly 83 Mb of data

There were 2 warnings

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Gabba Gabba Hey!" (The Ramones)

md.mdp文件参数为：
title = OPLS Lysozyme MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)
dt       = 0.002 ; 2 fs
; Output control
nstxout          = 5000 ; save coordinates every 10.0 ps
nstvout          = 5000 ; save velocities every 10.0 ps
nstenergy          = 5000 ; save energies every 10.0 ps
nstlog          = 5000 ; update log file every 10.0 ps
nstxout-compressed  = 5000    ; save compressed coordinates every 10.0 ps
                              ; nstxout-compressed replaces nstxtcout
compressed-x-grps = System ; replaces xtc-grps
; 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
cutoff-scheme = Verlet
ns_type       = grid ; search neighboring grid cells
nstlist       = 10       ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb       = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw       = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
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             ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1    0.1          ; time constant, in ps
ref_t = 300    300          ; 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

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