Just to confirm to everyone...
If you have applied bugfix.26 (or bugfix.all that includes bugfix.26) then
the ig=-1 option will be working fine. If you have not applied this to your
AMBER 10 then you will get the random number seed always set to -1. The
simple test for this is to check your mdout files and see what the ig value
is set to. If it is a value other than -1 then you are in good shape.
I will update the webpage now to add a note that this bugfix.26 addresses
this.
All the best
Ross
> -----Original Message-----
> From: Dean Cuebas [mailto:deancuebas.missouristate.edu]
> Sent: Friday, August 13, 2010 3:16 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] random number seed - range
>
> Dear list,
>
> I was also very concerned about the ig=-1 issue with pmemd10.
>
> But I checked the .out file for successive 2nsec runs and was easily
> able to
> confirm (or refute) that the random number generator was working.
>
> Luckily, mine was working :-)
>
> Dean
> --
> Dr. Dean Cuebas, Associate Prof of Chemistry
> deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
> > From: Robert Duke <rduke.email.unc.edu>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > Date: Fri, 13 Aug 2010 17:05:34 -0500
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] random number seed - range
> >
> > Yes, sorry for the confusion; per the previous mail from Ross, this
> was
> > buried in a bugfix, and I did not know about it, as I did not do that
> bugfix
> > and it was not in the title. So I still think it is a good idea for
> folks
> > to be cautious about this one - I for one, at some point in the
> middle of
> > the release cycle, look at the bugfixes titles to see if they are
> > interesting, but don't patch unless I need the fix. So the default
> released
> > behaviour of pmemd 10 is what I have been warning about, and I still
> think
> > it is a good idea to beware of the potential problem. Sorry for the
> > confusion; hopefully we all have discussed it enough now that folks
> will be
> > forewarned (so bugfix 26 is a whopper of a fix that includes CHARMM
> support
> > which is not exactly needed by everyone in the world...).
> > Regards - Bob
> >
> > ----- Original Message -----
> > From: "Paul S. Nerenberg" <psn.berkeley.edu>
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Sent: Friday, August 13, 2010 5:58 PM
> > Subject: Re: [AMBER] random number seed - range
> >
> >
> >> Hi Bob,
> >>
> >> Like the other Bob (Hopkins), I also see random ig values printed in
> >> my mdout files when setting ig=-1 in my mdin files with pmemd 10 --
> as
> >> I shared on this list when this issue first came up a few weeks ago.
> >> So I'm not sure where those values are coming from, but they are
> >> definitely being generated by the program.
> >>
> >> From my end, I am reasonably certain that I am using pmemd 10 for
> two
> >> separate reasons: (1) the version number can be seen in the output
> >> files I shared [see my messages from July 24 and July 27] and (2) I
> >> compiled it several months before AMBER 11 was released. Unless we
> >> had some sort of rogue source code floating around in our lab, it
> was
> >> the AMBER 10 release...
> >>
> >> Best,
> >>
> >> Paul
> >>
> >>
> >> On Aug 13, 2010, at 2:40 PM, Robert Duke wrote:
> >>
> >>> Okay, I am confused by this. PMEMD 10, at least in the source I
> >>> have, and
> >>> all the bugfixes for 10 I have seen, sets ig to a constant unless
> you
> >>> specify it. If you specify a -1, then that gets used as the seed
> for
> >>> setting initial velocities (non-restart runs) and -1 + 1 = 0 gets
> >>> used in a
> >>> reseeding for things like the Langevin or Anderson thermostats
> (this
> >>> is off
> >>> the top of my head, so I may be missing something else). So I
> don't
> >>> know
> >>> what values you initially set, and what other values you may be
> >>> looking at.
> >>> Is it perhaps really pmemd 11 you are using? I don't want to lull
> >>> folks
> >>> into thinking this stuff works in pmemd 10 or earlier; AFAIK it
> >>> doesn't, my
> >>> knowledge based on looking at the source code tree and bugfixes.
> >>> And I see
> >>> know traps for catching a -1 and error exiting. The problem came
> >>> about
> >>> because I was not aware of the change being made in sander; poor
> >>> communication on the part of the developers (sorry).
> >>> Regards - Bob Duke
> >>> ----- Original Message -----
> >>> From: "Hopkins, Robert" <hopkins.uhcl.edu>
> >>> To: "AMBER Mailing List" <amber.ambermd.org>
> >>> Sent: Friday, August 13, 2010 5:03 PM
> >>> 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
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>>
> >>>> _______________________________________________
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> >>>>
> >>>
> >>>
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> >>
> >>
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Received on Fri Aug 13 2010 - 15:30:09 PDT
