Hi GT,
Are you using PMEMD or Sander? If I remember correctly pmemd in AMBER 10
does not support the use of ig=-1. Only Sander does. PMEMD from AMBER 11
supports the use of ig=-1.
All the best
Ross
> -----Original Message-----
> From: g t [mailto:sketchfoot.gmail.com]
> Sent: Saturday, July 24, 2010 12:46 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] random number seed - range
>
> Hi!
>
> Thanks for your quick reply. I checked the outfiles when ig was set to
> -1
> and they stated that ig had been set to -1 every instance, instead of a
> random number based upon the current time & date. I'm afraid I no
> longer
> have those files to post though.
>
> My version of AMBER is 10 and is running on linux Red Hat Enterprise
> Linux
> Server release 5.4. I'm afraid I do not know the compiler for sure, but
> suspect they may have used the comercial intel compiler & fortran
> options.
>
> I think the issue is probably due to the TI limitation you speak off in
> the
> second paragraph. If I do have to specify the ig value manually, what
> do you
> think would be an acceptable range?
>
> Thanks again,
> GT
>
> On 24 July 2010 14:22, case <case.biomaps.rutgers.edu> wrote:
>
> > On Sat, Jul 24, 2010, g t wrote:
> > >
> > > I am ruinning a TI calculation. When I set the random number seed
> value
> > to:
> > >
> > > ig = -1
> > >
> > > The number is not set randomly based on the current date & time.
> >
> > First, what is you evidence that "ig=-1" is not using a different
> seed for
> > each run? (The seed chosen is printed in the output file). This
> sounds
> > like
> > a bug, but we need to know the version of Amber, the compiler
> (+version)
> > and
> > OS you are using.
> >
> > Second, note that you generally cannot use "ig=-1" for TI, since the
> > integration scheme (which depends on ig for ntt=3) needs to be the
> same
> > for each of the two groups. So, for TI, you have to manually choose
> a
> > different seed for each run, and make it the same in the two mdin
> files.
> >
> > ....dac
> >
> >
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Received on Sat Jul 24 2010 - 16:30:03 PDT
