[gmx-users] H-bond autocorrelation doubts

[André Farias de Moura]

that temperature has nothing to do with the simulation itself, so the ACF will
not change (it is meant for the analysis of Gibbs energy associated with the
breaking of that hydrogen bond you are analysing).

best

Andre

On Mon, Feb 28, 2011 at 2:01 PM, bipin singh <bipinelmat at gmail.com> wrote:
> Thanks for your suggestions.....
> Can you please give some explanation for my second doubt...
>
> 2011/2/28 André Farias de Moura <moura at ufscar.br>
>>
>> the manual does not enclose all the necessary knowledge for any kind of MD
>> simulation or analyses, so you have to read some papers and textbooks as
>> well.as I've already pointed out, g_hbond reads the whole set of frames,
>> but the
>>
>> results are meaningful (in the sense of having a homogeneous variance)
>> only
>> up to half of the size of the sample. if you need the correlation
>> function for a
>> longer time lag, increase the length of your simulation. that way, your
>> ACF
>> should remain meaningful.
>>
>> best
>>
>> Andre
>>
>> On Mon, Feb 28, 2011 at 10:36 AM, bipin singh <bipinelmat at gmail.com>
>> wrote:
>> >
>> > Hello,
>> >
>> > I am usng g_hbond to calculate H bond auto correlation during the
>> > simulation
>> > for two residues in my system, I have two doubts regarding this:
>> >
>> > 1)How to use -acflen to calculate autocorrelation for all the frames
>> > instead
>> > of half of the frames
>> > 2) What is the use of -temp option in calculating the autocorrelation
>> > because it is giving same result whether you use 298K or 500K
>> >
>> > I have read the manual but I am not clear about these functions.
>> > --
>> > ---------------------------------
>> > Thanks and regards
>> > Bipin Singh
>> >
>> >
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>
>
> --
> ---------------------------------
> Thanks and regards
> Bipin Singh
>
>
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