[gmx-users] countinuation run problem

Anthony Cruz acb15885 at uprm.edu
Fri Feb 24 17:04:20 CET 2006


On Thursday 23 February 2006 5:51 am, David van der Spoel wrote:
> Anthony Cruz wrote:
> > HI:
> > Yesterday one of my simulation crash. I check the log file. This are the
> > last lines of the file:
> >
> > Step           Time         Lambda
> >         6109000    12218.00098        0.00000
> >
> >    Rel. Constraint Deviation:  Max    between atoms     RMS
> >        Before LINCS         0.058792   1139   1140   0.007195
> >         After LINCS         0.000126     75     77   0.000021
> >
> >    Energies (kJ/mol)
> >        G96Angle    Proper Dih.  Improper Dih.          LJ-14    
> > Coulomb-14 3.95784e+03    1.69609e+03    1.21916e+03    7.85820e+02   
> > 3.20988e+04 LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)     
> > Potential 2.49591e+05   -7.40570e+03   -1.58839e+06   -2.16905e+05  
> > -1.52336e+06 Kinetic En.   Total Energy    Temperature Pressure (bar)
> >     2.74080e+05   -1.24927e+06    2.97765e+02   -8.69934e+00
> >
> > Then I try to use tpbconvert to continue the simulation by the following
> > command:
> >
> > -bash-2.05b$ tpbconv -f 1scnMD_MV.trr -e 1scn_MD_ENER.edr -s
> > 1scn_MD_TPR.tpr -o 1scn_MD_TPR_CONT.tpr
> >
> >                          :-)  G  R  O  M  A  C  S  (-:
> >
> >                                Grunge ROck MAChoS
> >
> >                             :-)  VERSION 3.2.1  (-:
> >
> >       Written by David van der Spoel, Erik Lindahl, Berk Hess, and
> > others. Copyright (c) 1991-2000, University of Groningen, The
> > Netherlands. Copyright (c) 2001-2004, 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.
> >
> >                                :-)  tpbconv  (-:
> >
> > Option     Filename  Type         Description
> > ------------------------------------------------------------
> >   -s 1scn_MD_TPR.tpr  Input        Generic run input: tpr tpb tpa xml
> >   -f  1scnMD_MV.trr  Input, Opt!  Full precision trajectory: trr trj
> >   -e 1scn_MD_ENER.edr  Input, Opt!  Generic energy: edr ene
> >   -n      index.ndx  Input, Opt.  Index file
> >   -o 1scn_MD_TPR_CONT.tpr  Output       Generic run input: tpr tpb tpa
> > xml
> >
> >       Option   Type  Value  Description
> > ------------------------------------------------------
> >       -[no]h   bool     no  Print help info and quit
> >       -[no]X   bool     no  Use dialog box GUI to edit command line
> > options -nice    int      0  Set the nicelevel
> >        -time   real     -1  Continue from frame at this time (ps) instead
> > of the last frame
> >      -extend   real      0  Extend runtime by this amount (ps)
> >       -until   real      0  Extend runtime until this ending time (ps)
> >   -[no]zeroq   bool     no  Set the charges of a group (from the index)
> > to zero
> > -[no]unconstrained
> >                bool    yes  For a continuous trajectory, the constraints
> >                             should not be solved before the first step
> >                             (default)
> >
> > Reading toplogy and shit from 1scn_MD_TPR.tpr
> > Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
> > Modifying ir->bUncStart to TRUE
> >
> > READING COORDS, VELS AND BOX FROM TRAJECTORY 1scnMD_MV.trr...
> >
> > trn version: GMX_trn_file (single precision)
> > Read frame   2334: step 1166500 time 2333.000
> >
> > Using frame of step 1166500 time 2333
> > Opened 1scn_MD_ENER.edr as single precision energy file
> > Reading frame   2330 time 2330.000
> >
> > READ 3 PRESSURE COUPLING MU'S FROM 1scn_MD_ENER.edr
> >
> >
> > READ 4 TEMPERATURE COUPLING LAMBDAS FROM 1scn_MD_ENER.edr
> >
> > 10083500 steps (20167 ps) remaining from first run.
> > Writing statusfile with starting step    1166500 and length   10083500
> > steps...
> >                                  time   2333.000 and length  20167.000 ps
> >
> > Back Off! I just backed up 1scn_MD_TPR_CONT.tpr to
> > ./#1scn_MD_TPR_CONT.tpr.1#
> >
> > gcq#162: "Rub It Right Accross Your Eyes" (F. Zappa)
> >
> >
> > The total time of my simulation is 22ns and as the log file said it runs
> > for Step           Time         Lambda
> >         6109000    12218.00098        0.00000
> > but  tpbconv use time   2333.000 and length  20167.000 ps for the
> > continue file. The output control in my mdp file are the fallowing:
> >
> >   ; Output Control
> > nstxout             =  500
> > nstvout             =  500
> > nstfout             =  0
> > nstlog              =  500
> > nstenergy           =  500
> >
> >
> > What is wrong?  Why do not continue at the last frame described in the
> > log file??
> >
> > Best regards
> > Anthony
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> run gmxcheck on your edr and trr files. Sometimes the OS buffers these
> files.
>
> maybe you have a full disk.


I run the gmxcheck and this is the oputput whe I use the trr file:

-bash-2.05b$ gmxcheck -f 1scnMD_MV.trr -c 1scn_MD_TPR.tpr -e 1scn_MD_ENER.edr 
>output
Option     Filename  Type         Description
------------------------------------------------------------
  -f  1scnMD_MV.trr  Input, Opt!  Generic trajectory: xtc trr trj gro g96 pdb
 -f2       traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96 pdb
 -s1       top1.tpr  Input, Opt.  Generic run input: tpr tpb tpa xml
 -s2       top2.tpr  Input, Opt.  Generic run input: tpr tpb tpa xml
  -c 1scn_MD_TPR.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
                                   pdb xml
  -e 1scn_MD_ENER.edr  Input, Opt!  Generic energy: edr ene
 -e2      ener2.edr  Input, Opt.  Generic energy: edr ene

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
     -vdwfac   real    0.8  Fraction of sum of VdW radii used as warning
                            cutoff
      -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  Relative tolerance for comparing real values
                            defined as 2*(a-b)/(|a|+|b|)
   -lastener string         Last energy term to compare (if not given all are
                            tested). It makes sense to go up until the
                            Pressure.

trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
# Atoms  110722
Last frame       2333 time 2333.000


Item        #frames Timestep (ps)
Step          2334    1
Time          2334    1
Lambda        2334    1
Coords        2334    1
Velocities    2334    1
Forces           0
Box           2334    1
Checking energy file 1scn_MD_ENER.edr

Opened 1scn_MD_ENER.edr as single precision energy file
frame:      0 (index      0), t:      0.000
Reading frame  12210 time 12210.001
Last frame read 12217
WARNING: Incomplete frame: nr  12218 time 12217.001


Found 12217 frames with a timestep of 1 ps.
Checking coordinate file 1scn_MD_TPR.tpr
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
110722 atoms in file
coordinates found
box         found
velocities  found

Kinetic energy: 411498 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 297.993 K or 446.99 K respectively.

Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
atom# name  residue r_vdw  atom# name  residue r_vdw  distance
   39   CA  PRO   5 0.15      41   CG  PRO   5 0.15   0.2354
   50  CD1  TYR   6 0.15      52  CD2  TYR   6 0.15   0.2392
   54  CE1  TYR   6 0.15      56  CE2  TYR   6 0.15   0.2398
   72  CG1  ILE   8 0.15      73  CG2  ILE   8 0.15   0.2366
   78   CA  PRO   9 0.15      80   CG  PRO   9 0.15   0.236
  191  CD1  PHE  21 0.15     193  CD2  PHE  21 0.15   0.2399
  191  CD1  PHE  21 0.15     199   CZ  PHE  21 0.15   0.2372
  193  CD2  PHE  21 0.15     199   CZ  PHE  21 0.15   0.2378
  242  CG1  VAL  26 0.15     243  CG2  VAL  26 0.15   0.2307
  263  CG1  VAL  28 0.15     264  CG2  VAL  28 0.15   0.2362
  352   CG HISB  39 0.15     355  CE1 HISB  39 0.15   0.2161
  354  CD2 HISB  39 0.15     355  CE1 HISB  39 0.15   0.2176
  381  CD1  LEU  42 0.15     382  CD2  LEU  42 0.15   0.2381
  415    C  GLY  46 0.15     419   CA  GLY  47 0.15   0.2385
  441  CD1  PHE  50 0.15     443  CD2  PHE  50 0.15   0.2366
  441  CD1  PHE  50 0.15     449   CZ  PHE  50 0.15   0.2359
  443  CD2  PHE  50 0.15     449   CZ  PHE  50 0.15   0.2365
  493  CD1  TYR  56 0.15     495  CD2  TYR  56 0.15   0.235
  497  CE1  TYR  56 0.15     499  CE2  TYR  56 0.15   0.2387
  560   CG HISA  63 0.15     564  CE1 HISA  63 0.15   0.2189
  563  CD2 HISA  63 0.15     564  CE1 HISA  63 0.15   0.2187
  586   CG HISB  66 0.15     589  CE1 HISB  66 0.15   0.2114
  588  CD2 HISB  66 0.15     589  CE1 HISB  66 0.15   0.215
  732   CB  PRO  85 0.15     734   CD  PRO  85 0.15   0.233
  774   CG  TYR  90 0.15     781  CE2  TYR  90 0.15   0.2377
  775  CD1  TYR  90 0.15     783   CZ  TYR  90 0.15   0.2344
  777  CD2  TYR  90 0.15     783   CZ  TYR  90 0.15   0.2392
  846   CB  SER  97 0.15     849    C  SER  97 0.15   0.2389
  889   CG  TYR 103 0.15     894  CE1  TYR 103 0.15   0.2375
  889   CG  TYR 103 0.15     896  CE2  TYR 103 0.15   0.2377
  969   CG  TRP 112 0.15     975  CE2  TRP 112 0.15   0.2196
  970  CD1  TRP 112 0.15     972  CD2  TRP 112 0.15   0.2191
  970  CD1  TRP 112 0.15     975  CE2  TRP 112 0.15   0.2134
  972  CD2  TRP 112 0.15     978  CZ2  TRP 112 0.15   0.2334
  976  CE3  TRP 112 0.15     982  CH2  TRP 112 0.15   0.2334
 1133    C  SER 131 0.15    1137   CA  THR 132 0.15   0.2385
 1148    C  ALA 133 0.15    1152   CA  MET 134 0.15   0.2399
 1210   CB  ASN 140 0.15    1216    C  ASN 140 0.15   0.2395
 1228   CG  TYR 142 0.15    1233  CE1  TYR 142 0.15   0.2358
 1228   CG  TYR 142 0.15    1235  CE2  TYR 142 0.15   0.2374
 1231  CD2  TYR 142 0.15    1237   CZ  TYR 142 0.15   0.2397
 1240    C  TYR 142 0.15    1244   CA  ALA 143 0.15   0.2358
 1297   CB  VAL 149 0.15    1300    C  VAL 149 0.15   0.239
 1414  CG1  ILE 164 0.15    1415  CG2  ILE 164 0.15   0.2399
 1428   CG  TYR 166 0.15    1433  CE1  TYR 166 0.15   0.2337
 1431  CD2  TYR 166 0.15    1437   CZ  TYR 166 0.15   0.2367
 1443   CA  PRO 167 0.15    1445   CG  PRO 167 0.15   0.2364
 1473  CD1  TYR 170 0.15    1481   CZ  TYR 170 0.15   0.2358
 1475  CD2  TYR 170 0.15    1481   CZ  TYR 170 0.15   0.2349
 1506   CB  VAL 173 0.15    1509    C  VAL 173 0.15   0.2383
 1635   CG  PHE 188 0.15    1640  CE1  PHE 188 0.15   0.2374
 1635   CG  PHE 188 0.15    1642  CE2  PHE 188 0.15   0.2383
 1636  CD1  PHE 188 0.15    1644   CZ  PHE 188 0.15   0.2397
 1638  CD2  PHE 188 0.15    1644   CZ  PHE 188 0.15   0.2385
 1737   CB  PRO 200 0.15    1739   CD  PRO 200 0.15   0.2391
 1760   CA  VAL 204 0.15    1763  CG2  VAL 204 0.15   0.2367
 1770   CG  TYR 205 0.15    1775  CE1  TYR 205 0.15   0.2387
 1770   CG  TYR 205 0.15    1777  CE2  TYR 205 0.15   0.2375
 1806  CD1  TYR 208 0.15    1808  CD2  TYR 208 0.15   0.2378
 1808  CD2  TYR 208 0.15    1814   CZ  TYR 208 0.15   0.2371
 1820   CA  PRO 209 0.15    1823   CD  PRO 209 0.15   0.2371
 1858   CB  TYR 213 0.15    1860  CD1  TYR 213 0.15   0.2399
 1859   CG  TYR 213 0.15    1864  CE1  TYR 213 0.15   0.2334
 1859   CG  TYR 213 0.15    1866  CE2  TYR 213 0.15   0.2349
 1864  CE1  TYR 213 0.15    1866  CE2  TYR 213 0.15   0.238
 1895    C  LEU 216 0.15    1899   CA  ASN 217 0.15   0.2391
 1964   CG HISA 225 0.15    1968  CE1 HISA 225 0.15   0.2109
 1967  CD2 HISA 225 0.15    1968  CE1 HISA 225 0.15   0.2122
 1970    C HISA 225 0.15    1974   CA  VAL 226 0.15   0.2388
 2048   CG LYSH 236 0.15    2050   CE LYSH 236 0.15   0.2377
 2061   CG HISB 237 0.15    2064  CE1 HISB 237 0.15   0.2181
 2063  CD2 HISB 237 0.15    2064  CE1 HISB 237 0.15   0.2159
 2070   CA  PRO 238 0.15    2072   CG  PRO 238 0.15   0.2335
 2188  CD1  LEU 249 0.15    2189  CD2  LEU 249 0.15   0.2392
 2236   CG  TYR 255 0.15    2241  CE1  TYR 255 0.15   0.24
 2237  CD1  TYR 255 0.15    2239  CD2  TYR 255 0.15   0.2369
 2239  CD2  TYR 255 0.15    2245   CZ  TYR 255 0.15   0.2361
 2284   CG  PHE 260 0.15    2289  CE1  PHE 260 0.15   0.239
 2284   CG  PHE 260 0.15    2291  CE2  PHE 260 0.15   0.2389
 2289  CE1  PHE 260 0.15    2291  CE2  PHE 260 0.15   0.239
 2302  CD1  TYR 261 0.15    2304  CD2  TYR 261 0.15   0.2383
 2302  CD1  TYR 261 0.15    2310   CZ  TYR 261 0.15   0.2396
 2306  CE1  TYR 261 0.15    2308  CE2  TYR 261 0.15   0.2397
 2319   CG  TYR 262 0.15    2324  CE1  TYR 262 0.15   0.2384
 2322  CD2  TYR 262 0.15    2328   CZ  TYR 262 0.15   0.2381
 2331    C  TYR 262 0.15    2335   CA  GLY 263 0.15   0.2379

Atoms outside box ( 10.4505 10.4505 10.4505 ):
(These may occur often and are normally not a problem)
atom# name  residue r_vdw  coordinate
 2433   OW  SOL 274 0.105 -0.027   5.42   3.13
 2435  HW2  SOL 274 0.04  -0.028   5.49    3.2
 2436   OW  SOL 275 0.105 -0.026   8.55   3.55
 2438  HW2  SOL 275 0.04  -0.035   8.46   3.49
 2439   OW  SOL 276 0.105 -0.025   10.3   1.25
 2442   OW  SOL 277 0.105 -0.025   9.44    8.7
 2443  HW1  SOL 277 0.04  -0.035   9.39   8.78
 2445   OW  SOL 278 0.105 -0.023   7.68   8.41
 2448   OW  SOL 279 0.105 -0.022  0.399   1.09
 2450  HW2  SOL 279 0.04  -0.037  0.341   1.17
(maybe more)


gcq#253: "(That makes 100 errors; please try again.)" (TeX)
==============================================================

I decide to run the gmxcheck with the xtc trajectory after the deshuffle with 
all the others files and I have the following output:

-bash-2.05b$ gmxcheck -f 1scnMD_MV_imp.xtc -c 1scn_MD_TPR.tpr -e 
1scn_MD_ENER.edr >output2
Option     Filename  Type         Description
------------------------------------------------------------
  -f 1scnMD_MV_imp.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       top1.tpr  Input, Opt.  Generic run input: tpr tpb tpa xml
 -s2       top2.tpr  Input, Opt.  Generic run input: tpr tpb tpa xml
  -c 1scn_MD_TPR.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
                                   pdb xml
  -e 1scn_MD_ENER.edr  Input, Opt!  Generic energy: edr ene
 -e2      ener2.edr  Input, Opt.  Generic energy: edr ene

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
     -vdwfac   real    0.8  Fraction of sum of VdW radii used as warning
                            cutoff
      -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  Relative tolerance for comparing real values
                            defined as 2*(a-b)/(|a|+|b|)
   -lastener string         Last energy term to compare (if not given all are
                            tested). It makes sense to go up until the
                            Pressure.

Reading frame       0 time    0.000
# Atoms  2857
Precision 0.001 (nm)
Last frame      12218 time 12218.001


Item        #frames Timestep (ps)
Step         12219    1
Time         12219    1
Lambda           0
Coords       12219    1
Velocities       0
Forces           0
Box          12219    1
Checking energy file 1scn_MD_ENER.edr

Opened 1scn_MD_ENER.edr as single precision energy file
frame:      0 (index      0), t:      0.000
Reading frame  12210 time 12210.001
Last frame read 12217
WARNING: Incomplete frame: nr  12218 time 12217.001


Found 12217 frames with a timestep of 1 ps.
Checking coordinate file 1scn_MD_TPR.tpr
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
110722 atoms in file
coordinates found
box         found
velocities  found

Kinetic energy: 411498 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 297.993 K or 446.99 K respectively.

Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
atom# name  residue r_vdw  atom# name  residue r_vdw  distance
   39   CA  PRO   5 0.15      41   CG  PRO   5 0.15   0.2354
   50  CD1  TYR   6 0.15      52  CD2  TYR   6 0.15   0.2392
   54  CE1  TYR   6 0.15      56  CE2  TYR   6 0.15   0.2398
   72  CG1  ILE   8 0.15      73  CG2  ILE   8 0.15   0.2366
   78   CA  PRO   9 0.15      80   CG  PRO   9 0.15   0.236
  191  CD1  PHE  21 0.15     193  CD2  PHE  21 0.15   0.2399
  191  CD1  PHE  21 0.15     199   CZ  PHE  21 0.15   0.2372
  193  CD2  PHE  21 0.15     199   CZ  PHE  21 0.15   0.2378
  242  CG1  VAL  26 0.15     243  CG2  VAL  26 0.15   0.2307
  263  CG1  VAL  28 0.15     264  CG2  VAL  28 0.15   0.2362
  352   CG HISB  39 0.15     355  CE1 HISB  39 0.15   0.2161
  354  CD2 HISB  39 0.15     355  CE1 HISB  39 0.15   0.2176
  381  CD1  LEU  42 0.15     382  CD2  LEU  42 0.15   0.2381
  415    C  GLY  46 0.15     419   CA  GLY  47 0.15   0.2385
  441  CD1  PHE  50 0.15     443  CD2  PHE  50 0.15   0.2366
  441  CD1  PHE  50 0.15     449   CZ  PHE  50 0.15   0.2359
  443  CD2  PHE  50 0.15     449   CZ  PHE  50 0.15   0.2365
  493  CD1  TYR  56 0.15     495  CD2  TYR  56 0.15   0.235
  497  CE1  TYR  56 0.15     499  CE2  TYR  56 0.15   0.2387
  560   CG HISA  63 0.15     564  CE1 HISA  63 0.15   0.2189
  563  CD2 HISA  63 0.15     564  CE1 HISA  63 0.15   0.2187
  586   CG HISB  66 0.15     589  CE1 HISB  66 0.15   0.2114
  588  CD2 HISB  66 0.15     589  CE1 HISB  66 0.15   0.215
  732   CB  PRO  85 0.15     734   CD  PRO  85 0.15   0.233
  774   CG  TYR  90 0.15     781  CE2  TYR  90 0.15   0.2377
  775  CD1  TYR  90 0.15     783   CZ  TYR  90 0.15   0.2344
  777  CD2  TYR  90 0.15     783   CZ  TYR  90 0.15   0.2392
  846   CB  SER  97 0.15     849    C  SER  97 0.15   0.2389
  889   CG  TYR 103 0.15     894  CE1  TYR 103 0.15   0.2375
  889   CG  TYR 103 0.15     896  CE2  TYR 103 0.15   0.2377
  969   CG  TRP 112 0.15     975  CE2  TRP 112 0.15   0.2196
  970  CD1  TRP 112 0.15     972  CD2  TRP 112 0.15   0.2191
  970  CD1  TRP 112 0.15     975  CE2  TRP 112 0.15   0.2134
  972  CD2  TRP 112 0.15     978  CZ2  TRP 112 0.15   0.2334
  976  CE3  TRP 112 0.15     982  CH2  TRP 112 0.15   0.2334
 1133    C  SER 131 0.15    1137   CA  THR 132 0.15   0.2385
 1148    C  ALA 133 0.15    1152   CA  MET 134 0.15   0.2399
 1210   CB  ASN 140 0.15    1216    C  ASN 140 0.15   0.2395
 1228   CG  TYR 142 0.15    1233  CE1  TYR 142 0.15   0.2358
 1228   CG  TYR 142 0.15    1235  CE2  TYR 142 0.15   0.2374
 1231  CD2  TYR 142 0.15    1237   CZ  TYR 142 0.15   0.2397
 1240    C  TYR 142 0.15    1244   CA  ALA 143 0.15   0.2358
 1297   CB  VAL 149 0.15    1300    C  VAL 149 0.15   0.239
 1414  CG1  ILE 164 0.15    1415  CG2  ILE 164 0.15   0.2399
 1428   CG  TYR 166 0.15    1433  CE1  TYR 166 0.15   0.2337
 1431  CD2  TYR 166 0.15    1437   CZ  TYR 166 0.15   0.2367
 1443   CA  PRO 167 0.15    1445   CG  PRO 167 0.15   0.2364
 1473  CD1  TYR 170 0.15    1481   CZ  TYR 170 0.15   0.2358
 1475  CD2  TYR 170 0.15    1481   CZ  TYR 170 0.15   0.2349
 1506   CB  VAL 173 0.15    1509    C  VAL 173 0.15   0.2383
 1635   CG  PHE 188 0.15    1640  CE1  PHE 188 0.15   0.2374
 1635   CG  PHE 188 0.15    1642  CE2  PHE 188 0.15   0.2383
 1636  CD1  PHE 188 0.15    1644   CZ  PHE 188 0.15   0.2397
 1638  CD2  PHE 188 0.15    1644   CZ  PHE 188 0.15   0.2385
 1737   CB  PRO 200 0.15    1739   CD  PRO 200 0.15   0.2391
 1760   CA  VAL 204 0.15    1763  CG2  VAL 204 0.15   0.2367
 1770   CG  TYR 205 0.15    1775  CE1  TYR 205 0.15   0.2387
 1770   CG  TYR 205 0.15    1777  CE2  TYR 205 0.15   0.2375
 1806  CD1  TYR 208 0.15    1808  CD2  TYR 208 0.15   0.2378
 1808  CD2  TYR 208 0.15    1814   CZ  TYR 208 0.15   0.2371
 1820   CA  PRO 209 0.15    1823   CD  PRO 209 0.15   0.2371
 1858   CB  TYR 213 0.15    1860  CD1  TYR 213 0.15   0.2399
 1859   CG  TYR 213 0.15    1864  CE1  TYR 213 0.15   0.2334
 1859   CG  TYR 213 0.15    1866  CE2  TYR 213 0.15   0.2349
 1864  CE1  TYR 213 0.15    1866  CE2  TYR 213 0.15   0.238
 1895    C  LEU 216 0.15    1899   CA  ASN 217 0.15   0.2391
 1964   CG HISA 225 0.15    1968  CE1 HISA 225 0.15   0.2109
 1967  CD2 HISA 225 0.15    1968  CE1 HISA 225 0.15   0.2122
 1970    C HISA 225 0.15    1974   CA  VAL 226 0.15   0.2388
 2048   CG LYSH 236 0.15    2050   CE LYSH 236 0.15   0.2377
 2061   CG HISB 237 0.15    2064  CE1 HISB 237 0.15   0.2181
 2063  CD2 HISB 237 0.15    2064  CE1 HISB 237 0.15   0.2159
 2070   CA  PRO 238 0.15    2072   CG  PRO 238 0.15   0.2335
 2188  CD1  LEU 249 0.15    2189  CD2  LEU 249 0.15   0.2392
 2236   CG  TYR 255 0.15    2241  CE1  TYR 255 0.15   0.24
 2237  CD1  TYR 255 0.15    2239  CD2  TYR 255 0.15   0.2369
 2239  CD2  TYR 255 0.15    2245   CZ  TYR 255 0.15   0.2361
 2284   CG  PHE 260 0.15    2289  CE1  PHE 260 0.15   0.239
 2284   CG  PHE 260 0.15    2291  CE2  PHE 260 0.15   0.2389
 2289  CE1  PHE 260 0.15    2291  CE2  PHE 260 0.15   0.239
 2302  CD1  TYR 261 0.15    2304  CD2  TYR 261 0.15   0.2383
 2302  CD1  TYR 261 0.15    2310   CZ  TYR 261 0.15   0.2396
 2306  CE1  TYR 261 0.15    2308  CE2  TYR 261 0.15   0.2397
 2319   CG  TYR 262 0.15    2324  CE1  TYR 262 0.15   0.2384
 2322  CD2  TYR 262 0.15    2328   CZ  TYR 262 0.15   0.2381
 2331    C  TYR 262 0.15    2335   CA  GLY 263 0.15   0.2379

Atoms outside box ( 10.4505 10.4505 10.4505 ):
(These may occur often and are normally not a problem)
atom# name  residue r_vdw  coordinate
 2433   OW  SOL 274 0.105 -0.027   5.42   3.13
 2435  HW2  SOL 274 0.04  -0.028   5.49    3.2
 2436   OW  SOL 275 0.105 -0.026   8.55   3.55
 2438  HW2  SOL 275 0.04  -0.035   8.46   3.49
 2439   OW  SOL 276 0.105 -0.025   10.3   1.25
 2442   OW  SOL 277 0.105 -0.025   9.44    8.7
 2443  HW1  SOL 277 0.04  -0.035   9.39   8.78
 2445   OW  SOL 278 0.105 -0.023   7.68   8.41
 2448   OW  SOL 279 0.105 -0.022  0.399   1.09
 2450  HW2  SOL 279 0.04  -0.037  0.341   1.17
(maybe more)


gcq#286: "Lets Kill the Fucking Band"  ( Tom Savini - From Dusk til Dawn )
===============================================================

As could be seen this way the program see the correct time from the 
trajectory. This could be due to the deshuffle??? What could cause this???

Best regards
Anthony



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