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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>
>
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Received on Fri Aug 13 2010 - 14:30:03 PDT
