[gmx-users] Warning: correlations not long enough
David van der Spoel
spoel at xray.bmc.uu.se
Fri Sep 7 08:14:00 CEST 2018
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
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.
More information about the gromacs.org_gmx-users