[gmx-users] Same starting structure but different trajectories

Emanuel Peter Emanuel.Peter at chemie.uni-regensburg.de
Wed Feb 17 09:56:14 CET 2010

Hi Tsjerk,

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 >>>
Hi Emanuel,

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.

Computational Chemist
Medicinal Chemist
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