ntr will freeze both, including their relative position. if you are trying
to optimize the position, why do you need restraints? don't you just want to
allow them to come close on their own?
if you do want to restrain, a distance restraint between the centers of
mass might help- you could bring it together slowly using the "nmr"
restraints with nmropt=1. look in the manual for details.
On Sat, Jul 9, 2011 at 7:19 AM, Eliac Brown <eliacbrown.yahoo.com> wrote:
> Dear AMBER
> My system is very simple, contains two molecules. I am studying the
> interaction between them using amber force field.
> I was wondering if I applied ntr constrain on each molecule (0.5 kcal/mol),
> does it give an opportunity for the two molecules to be optimized (come
> closer to each other based on the vdw interaction), or the ntr option will
> freeze the two molecules at their position? If it is the latter case, so
> what keyword/trick can I use?
> Thanks in advance, Eliac
>
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Received on Sat Jul 09 2011 - 04:30:04 PDT
