AMBER Archive (2009)

Subject: [AMBER] question

From: lev kantorovich (
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
King's College London
The Strand,
London, WC2R 2LS
United Kingdom
tel: +44-(0)2078482160
fax: +44-(0)2078482420

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