Aha, buried in a bugfix without being called out in the title... That
explains it. Thanks for clarifying; I am sure a few folks other than me
missed this...
Regards - Bob
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: "'AMBER Mailing List'" <amber.ambermd.org>
Sent: Friday, August 13, 2010 5:55 PM
Subject: Re: [AMBER] random number seed - range
> 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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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
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Received on Fri Aug 13 2010 - 15:00:07 PDT
