That's odd, unless the values are -666. I just looked at the source
code, and it seems as if the temperature is passed on to the right
functions.
Erik
bipin singh skrev 2011-02-28 19.34:
NO, its giving same result no matter what temperature you provide
using -temp option.
On Mon, Feb 28, 2011 at 23:55, Erik Marklund <[email protected]
<mailto:[email protected]>> wrote:
It computes the same acf, but the thermodynamic/kinetic
calculations give different results for different -temp, don't they?
Erik
bipin singh skrev 2011-02-28 18.01:
Thanks for your suggestions.....
Can you please give some explanation for my second doubt...
2011/2/28 André Farias de Moura <[email protected]
<mailto:[email protected]>>
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 <http://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
<[email protected] <mailto:[email protected]>> 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/
/
/
/
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] <mailto:[email protected]>
http://folding.bmc.uu.se/
--
/
---------------------------------
Thanks and regards
/Bipin Singh/
/
/
/
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
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