AMBER Archive (2009)

Subject: [AMBER] question

From: lev kantorovich (lev.kantorovitch_at_kcl.ac.uk)
Date: Wed Jun 10 2009 - 09:20:08 CDT

Dear Developers/Users,

I am new to AMBER and am wondering if the following calculation is supported
in the existing version:

I need to run a specific MD simulation with the following features:

(1) periodic boundary conditions (2D or 3D); essentially, I have a
periodic monolayer of Guanine molecules

(2) there are 8 molecules in the unit cell forming two tetrads, each
tetrad consists of 4 molecules forming a
square so that you can imagine that the unit cell consists of two
squares with 4 molecules each;
we would like to run an MD simulation
with the angle between the two squares fixed. The angle cannot be
defined by just 3 atoms, more atoms should be
involved (e.g. 4 atoms from each tetrad, 8 altogether), however, many
definitions can be given. Is it possible?

(3) in the end, a thermodynamic integration will be performed with
respect to the generalised force
associated with this variable (the angle) - however, this is easy to do
separately , so no problem here.

(4) can one calculate the vibrations for the given geometry? Most likely
- yes.

(5) are H-bonding interactions between Guanine molecules described
reasonably well? Which force
field (from those implemented) should be best for that system?

I'd appreciate your quick answer to these questions,

Best wishes, 

-- 
Lev Kantorovich
Physics
King's College London
The Strand,
London, WC2R 2LS
United Kingdom
tel: +44-(0)2078482160
fax: +44-(0)2078482420
email: lev.kantorovitch_at_kcl.ac.uk

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