[gmx-users] Frames problem

s lal badshah shahbiochemist at yahoo.com
Mon Jun 16 08:24:21 CEST 2008

Hi All,
I have MD simulation which crashed and I combine the frames with trjconv. Now the problem is that when I do analysis like that of Solvent accessible surface area, it showed that the incomplete frame . I use the gmxcheck with the following result
d 1: 'Protein'
1695 out of 2854 atoms were classified as hydrophobic
Reading frame      20 time  400.000   
WARNING: Incomplete frame: nr 28 time 560

gcq#190: "That Was Cool" (Beavis and Butthead)

lalbadshah at linux:~/323> gmxcheck -f md323.xtc -s1 md323.tpr -e md323.edr
                         :-)  G  R  O  M  A  C  S  (-:

           Glycine aRginine prOline Methionine Alanine Cystine Serine

                            :-)  VERSION 3.3.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, The GROMACS development team,
            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 General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  gmxcheck  (-:

Option     Filename  Type         Description
  -f      md323.xtc  Input, Opt!  Generic trajectory: xtc trr trj gro g96 pdb
 -f2       traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96 pdb
 -s1      md323.tpr  Input, Opt!  Generic run input: tpr tpb tpa xml
 -s2       top2.tpr  Input, Opt.  Generic run input: tpr tpb tpa xml
  -c      topol.tpr  Input, Opt.  Structure+mass(db): tpr tpb tpa gro g96 pdb
  -e      md323.edr  Input, Opt!  Generic energy: edr ene
 -e2      ener2.edr  Input, Opt.  Generic energy: edr ene
  -n      index.ndx  Input, Opt.  Index file

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
       -nice    int      0  Set the nicelevel
     -vdwfac   real    0.8  Fraction of sum of VdW radii used as warning
      -bonlo   real    0.4  Min. fract. of sum of VdW radii for bonded atoms
      -bonhi   real    0.7  Max. fract. of sum of VdW radii for bonded atoms
        -tol   real  0.001  Relative tolerance for comparing real values
                            defined as 2*(a-b)/(|a|+|b|)
     -[no]ab   bool     no  Compare the A and B topology from one file
   -lastener string         Last energy term to compare (if not given all are
                            tested). It makes sense to go up until the

Reading file md323.tpr, VERSION 3.3.1 (single precision)
Checking file md323.xtc
Reading frame       0 time    0.000   
# Atoms  37959
Precision 0.001 (nm)
Reading frame      20 time  400.000   
WARNING: Incomplete frame: nr 28 time 560

Item        #frames Timestep (ps)
Step            28    20
Time            28    20
Lambda           0
Coords          28    20
Velocities       0
Forces           0
Box             28    20
Checking energy file md323.edr

Opened md323.edr as single precision energy file
frame:      0 (index      0), t:      0.000  
Last frame read 500 time 1000.000            

Found 501 frames with a timestep of 2 ps.

gcq#58: "You Look Better Upside Down" (Throwing Muses)

Now what should I do? Please guide me.


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