[gmx-users] persistent jumps in trajectories

morpheus morpheus.sommer2008 at gmail.com
Wed May 4 12:12:39 CEST 2016


I'm having problems getting jumps out of my trajectories. Usually I follow
the suggestion of the Gromacs website (
and convert my trajectories with the perl script below: remove water, make
it whole, cluster, nojump, center and fit.

For previous projects these steps always did the job right.

But unfortunately this does not work for long simulations (1500 ns) of
PDB-ID 2RVD (a peptide of only 10 amino acids). I have performed the
simulation multiple times and after about 300-500 ns the jumps  still start
even after processing the trajectories as given below. With jumps I mean
this: http://s32.postimg.org/z8p90wf51/jump.jpg

Doing analysis on the trajectories with e.g. g_dist yields “There were 4
inconsistent shifts. Check your topology”.

I am wondering what I am doing wrong and how can I fix the trajectories?

Here is the script that I am usually using:

my $bn = $ARGV[0]; # base name

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f ".$bn.".md.xtc -s
".$bn.".md.tpr -o ".$bn.".noWater.md.xtc -skip 10 << Ende \n1\n1\n << Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f ".$bn.".noWater.md.xtc
-s ".$bn.".md.tpr -o ".$bn.".noWater.whole.md.xtc -pbc whole << Ende
\n1\n1\n << Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.md.xtc -s ".$bn.".md.tpr -o
".$bn.".noWater.whole.cluster.md.xtc -pbc cluster << Ende \n1\n1\n << Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.cluster.md.xtc -s ".$bn.".md.tpr -o
".$bn.".noWater.whole.cluster.nojump.md.xtc -pbc nojump << Ende \n1\n1\n <<

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.cluster.nojump.md.xtc -s ".$bn.".md.tpr -o
".$bn.".noWater.whole.cluster.nojump.center.md.xtc -center << Ende \n1\n1\n
<< Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.cluster.nojump.center.md.xtc -s ".$bn.".md.tpr -o
".$bn.".final.md.xtc -fit rot+trans << Ende \n1\n1\n << Ende";

system $cmd;

Can anyone help?



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