[gmx-users] strange but true : How to explain and avoid?

Chetan Mahajan chetanvm10 at gmail.com
Tue Jul 8 00:28:39 CEST 2014

Dear All,

I recently made a molecular dynamics run of TiO2-water-sodium-formate
system of 12740 atoms. Then I extracted dump file from xtc file of
production run ( NPT, 300 K, 1 bar) using gmxdump command. THere are total
10001 frames. Now, I have found that some quote ( not error/warning) is
getting printed in the middle of the listed coordinates of last frame (end
of NPT run) in dump file, following quote gets printed:

           x[ 3129]={ 1.14500e+00,  3.43700e+00,  1.79100e+00}
           x[ 3130]={ 1.06200e+00,  3.30200e+00,  1.82800e+00}

gcq#252: "This is Tense !" (Star Wars Episode I The Phantom Menace)

      x[ 3131]={ 2.03000e-01,  2.49500e+00,  8.39800e+00}
            x[ 3132]={ 1.98000e-01,  2.54600e+00,  8.31200e+00}
            x[ 3133]={ 2.76000e-01,  2.53300e+00,  8.45500e+00}

Can anyone explain what's going on? How to correct this? I do not see any
errors or warnings in output file.  Following is the .mdp file of
production run, if anyone wants to have a look:

integrator               = md-vv
dt                       = 0.002
nsteps                   = 2500000
nstxout                  = 1000
nstvout                  = 1000
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 250
nstlist                  = 1
ns-type                  = grid
rlist                    = 1.0
vdwtype                  = user
coulombtype              = pme
rcoulomb                 = 1.0
rvdw                     = 1.0
energygrps               = Ti OT OW c h5 o HW Na
energygrp-table          = Ti Ti OT OT Ti OT Ti OW OT c OT h5 OT o
tcoupl                   = nose-hoover
tc-grps                  = System
tau-t                    = 0.5
ref-t                    = 300
pcoupl                   = no


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