Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?

From: Jianing <song_jianing_hi.126.com>
Date: Tue, 13 Apr 2010 21:25:29 +0800 (CST)

Hi Case,
Thank you very much for your reply, especially for your recommending refrence book. I will search the articles and explore my problem.
Sincerely,
Jianing




2010-04-13 19:59:04case <case.biomaps.rutgers.edu> д
>On Tue, Apr 13, 2010, Jianing wrote:
>
>> but maybe I have found the reason for this surprising phenomenon, and I
>> need you to give a juge on this.
>> you know, writing every 4fs for 3.5ns is a very large mdcrd file,
>> especially when the trajectory is not a binary file, so I just cut
>> it into hunderds of pieces. That is, when sander finishes every 10ps
>> interval,it will output md1.rst, then, when do the next 10ps, the
>> initial coordinates is from md1.rst. and this cycle lasts until 3.5ns is
>> reached. Although this is proceeded by computer automatically, this may
>> also bright in errors, because the data accuracy is different between
>> calculating and reading data in sander, which I didn't know before.
>
>OK -- my bet is that you are seeing the Langevin problem, since you are using
>ntt=3. You *must* use a different random number each restart (or set ig=-1).
>See:
>
>.Article{Sindhikara09,
> author = {Sindhikara, D.J. and Kim, S. and Voter, A.F. and Roitberg, A.E.},
> title = {{Bad seeds sprout perilous dynamics: Stochastic thermostat induced
>trajectory synchronization in biomolecules}},
> journal = {J. Chem. Theory Comput.},
> volume = {5},
> pages = {1624-1631},
> year = {2009}
>}
>
>and earlier articles referred to there.
>
>[developers: is there any good reason we should make the default value be
>-1 for ig?]
>
>...good luck.....dac
>
>
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Received on Tue Apr 13 2010 - 06:30:03 PDT
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