[gmx-users] Warning: correlations not long enough

[Apramita Chand]

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
frequency.
 I used -ac option and obtained the forward lifetime.



Regards,
Apramita



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>
Content-Type: text/plain; charset=windows-1252; format=flowed

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
acf
> 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
lowered
> 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
> Apramita
>


-- 
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.
http://www.icm.uu.se


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