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
matter.
Carlos
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?
>
>Thanks,
>
>Grace
>
>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
>>Ross
>>
>>/\
>>\/
>>|\oss Walker
>>
>>| Department of Molecular Biology TPC15 |
>>| The Scripps Research Institute |
>>| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
>>| http://www.rosswalker.co.uk/ | PGP Key available on request |
>>
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Received on Wed Jul 21 2004 - 22:53:00 PDT
