[gmx-users] Same starting structure but different trajectories
Emanuel.Peter at chemie.uni-regensburg.de
Wed Feb 17 09:56:14 CET 2010
I ran my job on the same machine and made exactly the same inputstructure and
What does chaos mean in your opinion? A computer should do exactly the same
every time you start with the same starting conditions on the same machine.
I have to couple my ligand seperately and not as part of my protein, so I can't
couple just two groups named Protein and Non-Protein.
>>> Tsjerk Wassenaar 02/17/10 9:40 AM >>>
Anything small can cause trajectories to diverge, it's chaos. The
machine on which is run can make the difference. This is also covered
in the list archives.
> ;Temperature coupling
> tcoupl = nose-hoover
> tc-grps = protein NA+ CFP SOL
> tau_t = 0.1 0.1 0.1 0.1
> ref_t = 300 300 300 300
This is bad practice. Where did you get that from? Not from any _good_
tutorial, surely. Check
http://www.gromacs.org/Documentation/Terminology/Thermostats to learn
Tsjerk A. Wassenaar, Ph.D.
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