Hi Ifat,
I guess this is a jump over the periodic boundaries. You should remove
jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
Cheers,
Tsjerk
On Wed, Feb 16, 2011 at 10:19 AM, ifat shub shubi...@gmail.com wrote:
Hi,
I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
if the complex is seeing its next periodic image, so I used the g_mindist
command with the -pi option. My command line was:
g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
The output (see below) was stable until ~344ps when there is a jump in the
max internal distance (third column) from ~6nm to ~22nm. After the jump the
numbers are reduced back to ~6nm and remained stable until the run is
completed at 1ns.
Does anyone know how to explain this jump? Is this a real problem or just a
visualization artifact? Is there a way to avoid such jumps?
Here is the mdp file I used:
--run.mdp--
integrator = md
nsteps = 100
dt = 0.001
coulombtype = pme
vdw-type = cut-off
tcoupl = Berendsen
tc-grps = protein non-protein
tau-t = 0.1 0.1
ref-t = 310 310
nstxout = 100
nstvout = 0
nstxtcout = 100
nstenergy = 100
comm_mode = Linear ; Angular
comm_grps = Protein
xtc_grps = Protein
energygrps = Protein
--
Thanks,
Ifat
The output:
343.7 10.813 5.924 16.445 16.445 16.445
343.8 10.809 5.949 16.445 16.445 16.445
343.9 10.804 5.959 16.445 16.445 16.445
344 10.808 5.974 16.445 16.445 16.445
344.1 0.18 21.982 16.445 16.445 16.445
344.2 10.778 5.977 16.445 16.445 16.445
344.3 10.768 5.996 16.445 16.445 16.445
344.4 10.764 6.016 16.445 16.445 16.445
344.5 10.722 6.029 16.445 16.445 16.445
344.6 10.774 6.01 16.445 16.445 16.445
344.7 0.174 21.984 16.445 16.445 16.445
344.8 0.176 21.98 16.445 16.445 16.445
344.9 0.17 22.002 16.445 16.445 16.445
345 0.173 21.981 16.445 16.445 16.445
345.1 0.191 21.954 16.445 16.445 16.445
345.2 0.183 21.958 16.445 16.445 16.445
345.3 0.181 22.012 16.445 16.445 16.445
345.4 0.17 22.054 16.445 16.445 16.445
345.5 0.168 22.054 16.445 16.445 16.445
345.6 0.189 22.039 16.445 16.445 16.445
345.7 0.171 22.007 16.445 16.445 16.445
345.8 0.186 22.031 16.445 16.445 16.445
345.9 0.171 22.077 16.445 16.445 16.445
346 0.187 21.99 16.445 16.445 16.445
346.1 0.173 21.984 16.445 16.445 16.445
346.2 0.181 22.02 16.445 16.445 16.445
346.3 10.82 5.984 16.445 16.445 16.445
346.4 10.81 6.002 16.445 16.445 16.445
346.5 10.819 6.008 16.445 16.445 16.445
346.6 10.813 5.996 16.445 16.445 16.445
346.7 10.781 6.006 16.445 16.445 16.445
346.8 10.793 6.026 16.445 16.445 16.445
346.9 10.745 5.985 16.445 16.445 16.445
347 10.762 5.999 16.445 16.445 16.445
347.1 10.781 5.984 16.445 16.445 16.445
347.2 10.784 6.002 16.445 16.445 16.445
--
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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