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]> 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]> > >> 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 <[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 >> > >> > >> > -- >> > gmx-users mailing list [email protected] >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to [email protected]. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > * > --------------------------------- > 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 [email protected] > http://folding.bmc.uu.se/ > > -- * --------------------------------- Thanks and regards Bipin Singh * * *
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