Yes it is. I believe the NCSU codes do this (see the adaptively biased MD
sections in the amber10 manual). Another way of doing this is to use NMR
restraints. See page 108 in the Amber10 manual, which shows you how to set
up SMD using the nmropt setup. You can choose to set the first location as
the geometric center of coordinates of a group of atoms by setting that
value of iat to a negative value. For this description, see Chapter 6 of
the Amber10 manual. This shows you how to actually set up the restraints
(which can be used for steered MD). Set iat=-1,52, igr1=1,2,3,4,5,6, ... to
set up a distance restraint between the center of geometry of atoms 1, 2, 3,
4, 5, 6 (distance from) atom 52. You can likewise define the second iat
entry to another negative number and set igr2. This is detailed in the
manual. Another option is to use the natural language "restraint" keyword,
also described in Chapter 6 of the amber manual.
Hope this helps,
Jason
On Tue, Sep 14, 2010 at 10:09 AM, <eduardo.troche.uvigo.es> wrote:
> Hi everybody,
>
> I want to perform some steered molecular dynamics on a system composed
> by a cyclodextrin and a small molecule, and as i was searching for
> some info on how to do it, i saw that most people sets a coordinate
> axis on the center of the cyclodextrin, but most of them don't use
> AMBER.
> Is it possible to do such thing with AMBER 10?
>
> Thanks in advance
>
> Eduardo
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Sep 14 2010 - 11:00:03 PDT
