Re: AMBER: Is the MD simulation normal

From: Thomas E. Cheatham, III <>
Date: Thu, 26 May 2005 11:41:03 -0600 (Mountain Daylight Time)

> However, After 1 ns NPT MD, the two important hydrogen bonds were
> lost. I roughly measure the -- the distance between donor and
> receptor , the distance become 2 or 3 angstrom larger than the former
> distance.

If you were using constant pressure with restraints (NTR=1), then the
relative positions of the molecules may change due to pressure scaling.
To get around this, only restrain the protein and add in explicit hbond
restraints (using the NMR options) for the equilibration phase. There are
other work-arounds discussed in the archives.

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Received on Thu May 26 2005 - 18:53:00 PDT
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