[gmx-users] Re Warning- Correlations not long enough
apramita.chand at gmail.com
Tue Sep 11 12:20:50 CEST 2018
As suggested, I plotted the correlation function in xmgrace and it looks
fine. I used -fitfn option and also -smooth option ( which If >= 0,
smooths the tail of the ACF by fitting it to an exponential function: y =
Surprisingly, for all these options (or without) the same warning shows up
and the hbond lifetime obtained remains unchanged.
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001
Tail value (average C(t) over second half of acf): 0.00340811 +/- 0.00108356
Back Off! I just backed up hbac_30_pt.xvg to ./#hbac_30_pt.xvg.3#
Hydrogen bond thermodynamics at T = 300 K
Fitting parameters chi^2 = 0.00596444
Should I go with the lifetime obtained?
reply to :
Date: Sat, 8 Sep 2018 08:32:43 +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: <eb489850-a054-2e2b-e062-f72e29b6feaa at xray.bmc.uu.se>
Content-Type: text/plain; charset=windows-1252; format=flowed
Den 2018-09-07 kl. 17:33, skrev 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
> I used -ac option and obtained the forward lifetime.
That looks good, if you open the autocorrelation figure in xmgrace, does
it look good? Can you fit an exponential curve to it with a time
constant roughly like 45 ps?
If you are analyzing a HBond that is present during the whole simulation
the analysis will not give a meaningful result.
> 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
>> 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
>> and then this is calculated, can I quote this lifetime? Is it accurate?
>> Please help
>> Yours sincerely
More information about the gromacs.org_gmx-users