AMBER Archive (2004)

Subject: Re: AMBER: cut offs in amber?

From: Carlos Simmerling (
Date: Wed Jul 21 2004 - 16:32:18 CDT

I think what Ross meant was that it should not matter if you have a
periodic system and
use PME. In that case, the system acts as if there are not cutoffs at
all, so it doesn't

Grace Li wrote:

>Hi Ross,
>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.
> Wouldn't group based cutoff with shorter cut off be a better
>alternative in this case rather than atombased?
>On Wed, 21 Jul 2004, Ross Walker wrote:
>>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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