[gmx-users] drug-enzyme simulation.

[Justin A. Lemkul]

Neha Gandhi wrote:
> 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?

Did the protein and/or ligand cross a periodic boundary?  If so, trjconv can 
"fix" this visualization artifact.

-Justin

> Your help is much appreciated.
> 
> 
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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