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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--
========================================
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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