[gmx-users] Same starting structure but different trajectories

[Tsjerk Wassenaar]

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
more.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist