Let me turn your question around.
What do you expect your autocorrelation time to be for the water you are
looking at ? You should have thought of that before you ran the
calculation, so you could plan accordingly.
Whatever the autocorrelation time it is, you would need to save data
maybe 10 to 100 times more often that that, otherwise you miss the decay
and cannot compute what you want.
So yes, if the expected number is 1 ps for instance, you would need to
save structures every 10 fs or so.
Adrian
On 6/7/17 12:37 PM, ATUL KUMAR wrote:
> Thanks for reply.
> In my simulation I have saved trajectory at every 100 psec and time step of
> simulation is 2 fsec. So should I need to save trajectory at every 10-20
> fsec???
>
> On Jun 7, 2017 7:06 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>
>> George is right, and this information is in fact in the cpptraj
>> section of the Amber 17 manual (page 645):
>>
>> "[usevelocity] Use velocity information in frame if present. This will
>> only give sensible results if the velocities are recorded close to the
>> order of the simulation time step."
>>
>> -Dan
>>
>> On Wed, Jun 7, 2017 at 9:13 AM, George Giambasu <giambasu.gmail.com>
>> wrote:
>>> Your plot seems to capture only the long time behavior of the velocity
>> autocorrelation function (VAC). Water velocities de-correlate pretty
>> quickly: probably on ~10-50 fs time intervals and to get the full details
>> of the VAC you want o write the velocities with a higher frequency (few fs).
>>> George
>>>
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>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
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>>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Jun 07 2017 - 10:00:04 PDT
