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 - 15:00:06 PDT
