What decides the pulling direction in SMD?

From: 李璀 (letitgone_at_hotmail.com)
Date: Fri Jun 12 2009 - 02:35:15 CDT

Dear all,

    I am doing my SMD with a protein-ligand complex, while the protein has 2 ports for the ligand to escape. I firstly chose a velocity, about 0.5A/ps and a direction that the ligand could leave from the protein via port1 quickly, and the program did so. However, when I kept the direction but changed the velocity to a smaller one, about 0.03A/ps, the ligand got out from the other port--port2. And when the velocity changed to 0.01A/ps, the ligand came back to leave from port1 . I cant't understand what decides the direction of the pulling direction in SMD. Would anyone tell me? Thanks a lot.

 

                                                                                                Tracy Lee

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