[gmx-users] drug-enzyme simulation.

Neha Gandhi n.gandhiau at gmail.com
Sun Mar 29 01:59:45 CET 2009

Hi List,

1) I m running a drug -enzyme simulation. I ran 62 ps of simulated
annealing followed by  production runs of 5ns usng NPT and PBC and
PME.. After 5ns, the protein moves far away from the ligand.  I
checked the 4ns gro files, the ligand and protein are bound together,
but its only that 5ns gives issues.

2) I ran another similar but smaller system and the complex is stable
even after 8ns.

What went wrong with the simulations in case 1? Is there a way to fix
this problem?
Your help is much appreciated.

Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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