Re: [AMBER] regarding REMD

From: David A Case <case.biomaps.rutgers.edu>
Date: Fri, 11 May 2012 13:40:02 -0400

On Fri, May 11, 2012, Carlos Simmerling wrote:

> I agree with Jason all around, except for the ig=-1. I tend to set the seed
> explicitly just so I can more readily reproduce the simulations. it's not
> that I think ig=-1 is incorrect, I just feel more comfortable knowing that
> if I run the same input I will get the same output. It does take more work.

OK: my $.02 on this question: the program prints out the value of the seed
that it chose, so you can use this to re-run the job if needed, using the
printed seed.

It is true that this is not literally "the same input", so it is indeed
somewhat a matter of taste. But if there is any chance that you might
forget to reset "ig" for each run, I'd recommend using the -1 option.

....dac


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Received on Fri May 11 2012 - 11:00:04 PDT
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