[gmx-users] Warning: correlations not long enough

[David van der Spoel]

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