RE: AMBER: cut offs in amber?

From: Ross Walker <>
Date: Wed, 21 Jul 2004 14:39:47 -0700

Dear Grace,

> Thanks for your reply. I have a system that contains ions and it is
> critical to get the electrostatic interactions as accurate as
> possible. As
> I understand it, atom based cutoff can cause problems if the
> cut off is
> too short. My system is approximately 24 X 24 X 24, would a
> CUT = 9 be ok?
> The ions are simple molecular ions.

You don't say whether you are using periodic boundaries or not. With the
particle mesh Ewald system implemented in Sander the cut off value is only
used to limit the direct space sum and so it has a much smaller effect than
in gas phase where the cut off value is used to truncate non-bonded pairs on
an atom by atom basis. Thus if you are doing a periodic boundary simulation
a cut off of 9 will probably be ok. If you doing gas phase then you should
increase this to as large as you can computationally handle. Essentially the
larger the better. Try running a single step of minimisation and plotting
the energy as a function of cut off distance (see

You should choose a cut off distance larger than the point at which your
energy starts to converge.

> Wouldn't group based cutoff with shorter cut off be a better
> alternative in this case rather than atombased?

For gas phase yes it would as this would ensure that everything within the
cutoff for a single atom has a charge sum of zero. This is not the case with
an atom based cut off. However, this is not implemented within sander due to
the problems with maintaining separate non-bonded lists and update
mechanisms for gas phase vs non gas phase simulations. If you really need to
do a gas phase simulation and need residue based cut-offs you could try
using sander.QMMM (apply bugfix.13 first) and setting nqt=0. I have no idea
if this will actually work though so you'd have to try it. I believe
sander.classic that used to ship with older versions of amber also includes
residue based cut-offs, although I have not tried this.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jul 21 2004 - 22:53:00 PDT
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