AMBER Archive (2006)

Subject: AMBER: one question on MD

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sat Sep 23 2006 - 20:03:11 CDT

Dear all,

In one of my running on MD (5 ns), I find with the
time passing, the content of the sheet and helix
decreased significantly and the content of coil
increased. Is this caused by the instability of the
protein or by some other reasons?

In addition, for the sander command input, some
reference needs the -ref with file name same as
specified by -c, some reference does not need -c. Does
these produce any influence on the final results?

I am looking forward to getting your result.

Best regards.

Fenghui Fan

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