Well, 5 ns is not a long time in the life of a protein-peptide complex.
I would start several (5-10?) runs with different (random) starting
impulse to get more reliable data.
If the conformational change is connected to crossing a significant
energy barrier, it will be a rare event... which means you have to
sample longer in each run to have the chance to see it again.
You might use implicit solvent to see more of conformational space in
shorther time (possibly with somewhat elevated temperature)... also see
"simulated annealing".
Good luck and gongzuo yukuai,
Alex
Am 09.10.2012 11:17, schrieb Liu Shiyong:
Dear all,
I did a MD simulation (GROMACS 4.5 G53a6 force field) on
protein-peptide complex for 5ns and got an interesting conformational
change of T-loop.
However, when I rerun my script using the same input file in the same
machine, I can not observe the same or similar conformational change.
There is a significant difference between two independent run.
What could I do for inconsistent MD simulation?
Best
Shiyong
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