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-- 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 >>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>>> >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >> > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Aug 13 2010 - 15:30:06 PDT