Hi Robert,
Support for ig=-1 was added (somewhat silently) as part of bugfix.26 to
AMBER 10 PMEMD hence the reason you are okay. There would probably have been
a better way to do this in the first place, i.e. specifying something like
USE_WALLCLOCK for ig in the mdin file that would have caused an abort during
the namelist read if it wasn't supported. However, the ig=-1 option was
effectively silently added to the sander tree without any real mention of it
on the developers mailing list which is why it ended up the way it is.
At least in your case though you are good.
All the best
Ross
> -----Original Message-----
> From: Hopkins, Robert [mailto:hopkins.uhcl.edu]
> Sent: Friday, August 13, 2010 2:04 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] random number seed - range
>
> After having just completed over 240 ns of MD calculations on duplex
> DNA
> molecules using pmemd 10, I felt a certain amount of panic when I
> recently
> read that for ig=-1, the clock-based generation of a random number seed
> had not been implemented in pmemd 10. So, for any others who are using
> pmemd 10 and are concerned about problems arising from a constant
> default
> random number seed in calculations involving DNA, I'll add my "two
> cents"
> here.
>
> When I looked at the actual number being used for the random number
> seed
> (ig)
> in a series of calculations representing 40 ns, I found the following
> values
> for runs done at selected intervals of 5 ns:
>
> ns ig
>
> 5 84988
> 10 829000
> 15 637723
> 20 384269
> 25 113068
> 30 313712
> 35 466334
> 40 546673
>
> A definite feeling of relief!
>
> Bob Hopkins
>
>
> -----Original Message-----
> From: Robert Duke [mailto:rduke.email.unc.edu]
> Sent: Tuesday, July 27, 2010 2:13 PM
> To: AMBER Mailing List
> Subject: [Possible Spam: 10%] Re: [AMBER] random number seed - range
>
> Yes, I did not know that this functionality was going into amber 10
> sander,
> so I did not put it into pmemd 10, unfortunately (because it is
> definitely a
> source of some confusion). I think Ross' group put it into pmemd 11.
> Regards - Bob Duke
> ----- Original Message -----
> From: "case" <case.biomaps.rutgers.edu>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Tuesday, July 27, 2010 3:02 PM
> Subject: Re: [AMBER] random number seed - range
>
>
> > On Tue, Jul 27, 2010, Keith Van Nostrand wrote:
> >>
> >> Because of correlation in the data, I had started using ig = -1 as
> >> well. I am
> >> doing Langevin dynamics with Amber 10 pmemd, and my output shows ig
> =
> -1
> >> everywhere:
> >
> > As far as I can tell from a quick code check, the special handling of
> > ig=-1
> > in pmemd did not occur until Amber11. If anyone has more detailed
> info,
> > they
> > can post it here.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> >
> >
>
>
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Received on Fri Aug 13 2010 - 15:00:05 PDT
