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

[Roland Schulz]

Hi,

use -quiet (in 5.0) or 2>/dev/null

Roland


On Mon, Jul 7, 2014 at 6:28 PM, Chetan Mahajan <chetanvm10 at gmail.com> wrote:

> 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
>
>
> Thanks
> Chetan
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