AMBER Archive (2005)

Subject: Re: AMBER: How to fix the atom in NPT case?

From: David A. Case (case_at_scripps.edu)
Date: Tue May 03 2005 - 19:16:33 CDT

On Tue, May 03, 2005, george Chen wrote:

>
> MD1 simulation: the coordinates after 1ps simulation are (38.726,
> 25.826, 11.551), and the coordinates are (38.686, 25.799, 11.530)
> after 25ps run.
> MD2 simulation: the coordinates after 1ps (38.765, 25.782, 11.541) and
> the coordinates after 20ps (38.647, 25.761, 11.511)
> MD3 simulation: the coordinates after 1ps (38.743, 25.790, 11.507) and
> the coordinates after 20ps (38.655, 25.934, 11.563)
> MD4 simulation: the coordinates after 1ps (38.564, 25.856, 11.508) and
> the coordinates after 300ps (26.650, 19.707, 1.661)

So, the C10 stays fixed until sometime between 1ps and 300ps of the final
run. You should look visually to see what is happening. Also, look for a
large restraint energy: if C10 has moved by 10-20 Ang. in spite of the
restraint, you must have a large restraint energy. This is not something
that can easily be diagnosed from afar. My best guess is that when you
finally let the DNA go free, something very bad is happening, causing great
forces that are sufficient to overcome the restraint energy. My general
experience is that examining the trajectory closely in VMD or Moil-view is
often the best way to track down weird behavior.

...good luck....dac

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