The only change that I know must be made if one does not use shake is to
set the time step (dt) to .001 (ps), i.e. 1 fs, because the .002-ps step
leads to excessive changes in the bond lengths, especially for the heavy
atom-hydrogen bonds, and thus high energies. Since I'm just recently using
Amber 6.0, there might be some other changes listed in the manual as well.
Good luck!
Sincerely,
Michael Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, Georgia 30602, USA
On Wed, 7 Feb 2001, Eoin Galligan wrote:
> Dear all
> I'm am not using SHAKE in some dynamics due to previously encountered
> errors. However, I now face v.high energies ie they read "****". I have
> tried using shake on only h-bonds however without success. If shake is not
> used are there any other flags that are required?
>
> Regards, E.Galligan
>
>
> tel: 0115 9515151 ext 66272
> mobile: 07968 349629
> mobile email: eoingalligan_at_sms.genie.co.uk
> (160 char max)
>
> Laboratory of Biophysics and Surface Analysis,
> Institute of Pharmaceutical Sciences,
> Nottingham University,
> University Park,
> Nottingham,
> NG7 2RD,
> UK
>
>
>
>
Received on Wed Feb 07 2001 - 08:32:51 PST
