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

From: David A. Case <>
Date: Mon, 2 May 2005 11:31:26 -0700

On Mon, May 02, 2005, george Chen wrote:
> I have a question about the MD simulation by using Amber 8. I want to
> fix one of the molecules. Then I use NTR = 1 in the MD input file. In
> the case NTB=1 and NTP=0 (NVT condition), the change of the
> Coordinates of the atoms within the fixed molecule is minor. However,
> in the case NTB=2 and NTP=1 (NPT condition), the change of the
> coordinates of the atoms is significant.

What do you catergorize as significant? The restraints will allow small
changes in coodinates, but this should rarely be a problem.

> Hold the DNA and CNT fixed
> 500.0

This is way too big a force constant. Try something about 100 times smaller.

....good luck....dac

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Received on Mon May 02 2005 - 19:53:01 PDT
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