[gmx-users] Warning: correlations not long enough

[David van der Spoel]

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 <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