[gmx-users] Warning: correlations not long enough
apramita.chand at gmail.com
Fri Sep 7 17:34:05 CEST 2018
Dear Dr. Spoel,
Initially I used a 100ns simulation with 0.002 time step.
Then I tried a 10ns simulation with 0.0005 timestep and lower output
I used -ac option and obtained the forward lifetime.
Reply to :Message: 2
Date: Fri, 7 Sep 2018 08:14:48 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Warning: correlations not long enough
Message-ID: <ad407060-789d-bc24-354d-cbf089b8a9c7 at xray.bmc.uu.se>
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Den 2018-09-06 kl. 17:13, skrev Apramita Chand:
> Dear All,
> In my simulations ,I have a Peptide in aqueous solution with a cosolvent.
> For more number of hydrogen bonds like peptide water, water-water, there
> are no warnings
> But for Peptide cosolvent, there are 315 hydrogen bonds and it does the
> as 315/315...
> It shows warning: correlations not long enough
> My original time step was 0.002 and I changed it to 0.0005 and even
> the output frequency of coordinates
How long is the simulation? You do not have to store so often, may 50 fs
is enough, but you may need a longer simulation. If 45 ps is a realistic
correlation time you need at least some nanoseconds. And do not use the
-life option, as is described in my old JPCB 110 pp. 4393-4398 (2006).
> Doing so gave me a 80GB output file!
> Still the problem persists..
> The lifetime that is output on the screen is 45 ps.
> Since it writes that the lower half of the correlation function was fitted
> and then this is calculated, can I quote this lifetime? Is it accurate?
> Please help
> Yours sincerely
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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