Den 2018-09-11 kl. 17:54, skrev Apramita Chand:
Dear Dr.Spoel,
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 =
Aexp(-x/tau)
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?
The number is quite small, and if is this for one specific hydrogen bond
it will not get much better.
Yours sincerely,
Apramita
reply to :
Message: 2
Date: Sat, 8 Sep 2018 08:32:43 +0200
From: David van der Spoel <sp...@xray.bmc.uu.se>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Warning: correlations not long enough
Message-ID: <eb489850-a054-2e2b-e062-f72e29b6f...@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
frequency.
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.
Regards,
Apramita
Reply to :Message: 2
Date: Fri, 7 Sep 2018 08:14:48 +0200
From: David van der Spoel <sp...@xray.bmc.uu.se>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Warning: correlations not long enough
Message-ID: <ad407060-789d-bc24-354d-cbf089b8a...@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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