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
>>>>
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>
>>>
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>>
>>
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Received on Fri Aug 13 2010 - 15:30:03 PDT
