Tanping Li wrote:
Dear Tsjerk,
Thanks for your help.
I run the two jobs on a cluster, maybe on different
nodes;
After just a few hundreds ps, the coordinates of the
system differs a lot. When I calculate the distance
between two atoms, there is about 1.5A difference;
Everything else in mdp file is exactly same.
Have you checked the following:
gmxcheck -s1 top1.tpr -s2 top2.tpr
and verified that only the output parameters were different?
If so, please submit a bugzilla and upload the two tpr files.
Yours
Tanping
--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Tanping Li,
Can you be more elaborate? What are the differences?
What do you mean with
"totally different"? Did you run it on the same
machine? Was everything else
the same?
Cheers,
Tsjerk
On 10/5/07, Tanping Li <[EMAIL PROTECTED]> wrote:
Dear all,
I run a 1ns trajectory for a protein in water. by
accidence, I find that the minor different in mdp
file
gives two totally different trajectories. By
setting
nstxou=500
nstvou=500;
and
nstxou=2500
nstvou=2500;
There is very large difference between two
trajectories (dt=2fs in both cases). I am really
confused: nstxou JUST sets the frequency to output
the
coordinate, why I get different results? Looking
forward to your opinion and thanks a lot.
Yours
Tanping Li
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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