AMBER Archive (2006)

Subject: Re: AMBER: one question on MD

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Sat Sep 23 2006 - 20:32:46 CDT

It's impossible to answer. We don't know whether your initial
structure should be stable- is it an experimental structure?
We also don't know what force field you are using, what
solvent model, or what simulation paramters such as temperature.
You didn't say how you performed the equilibration phase.
Try to give us more info and we can help, but remember that
we are here to help with problems related to Amber. You
might have to read journal articles to find out about what kinds
of simulations work well for the research that you want to do..

Fenghui Fan wrote:

>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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