AMBER Archive (2005)

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

From: george Chen (georgemdchen_at_gmail.com)
Date: Mon May 02 2005 - 14:35:42 CDT

> 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
>

Dear Professor David,

Thank you very much for your kind reply. I use Four steps MD
simulation. The initial coordinates of one of the atoms is (38.057,
25.445, 11.095), the final coordinates after 2ns is (26.565, 19.519,
1.634). I think the changes in coodinates is too big. Maybe I should
recalculate it by using a small force constant. Thanks again.
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