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
