Think i now understand your question. Forget what i wrote before.
I could imagine the the 'grompp -t npt.cpt' part is a problem.
If the simulations would be numerical reproducible, one should get the
same results. As they are not, the results will differ somewhat (would
think the more, the
Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...
On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier schl...@uni-mainz.dewrote:
Think i now understand your question. Forget what i
Don't know. One idea i have: Take a flexible and a relative rigid system
and perform simulations with the same starting conditions (- using -t
*.cpt). I would imagine that for the flexible system the trajectories
start earlier to deviate, since more stuff could happen (system is more
flexible
I am not sure but different force profiles may be due to the
non-equilibrium relaxation problem. The path on the energy landscape during
the non-equilibrium simulations depends on the pulling rate and/or
relaxation of any unknown coordinates correlated with pulling coordinates.
If during pulling,
there should be an extra option in your mdrun command line if
reproducibility is an issue:
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
the value of -reprod is set to no by default, turn on that option and
trajectories should be the same.
best
Andre
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