AMBER Archive (2004)

Subject: RE: AMBER: cut offs in amber?

From: Ross Walker (
Date: Wed Jul 21 2004 - 16:05:02 CDT

Dear Grace,

> I would like to know if amber uses group based cut offs or
> not, if so is
> there an option to specify that in my md input file?

Sander versions 6, 7 and 8 all use atom based cut offs based purely on the
distance specified for the cut off value. This is efficient for periodic
boundary calculations but can cause problems with gas phase simulations. It
is not possible to specify residue or group based cut-offs.

However, sander.QMMM (version 8) uses residue based cut-offs. Any residue
which has at least 1 atoms inside the distance defined by CUT= has the
residue included in the non-bond calculations.

I hope this helps.
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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