[gmx-users] Regarding H-bond autocorrelation

[Erik Marklund]

Hi,

The problem is that g_hbond subtracts a "background level" to compensate for the finite size of the system. I thought that feature had been taken away, however. Are you using old code?

Erik

12 jun 2011 kl. 19.33 skrev bipin singh:

> Hello,
> 
> I am calculating the H-bond autocorrelation using g_hbond for my
> system, but after plotting
> I have observed that the value for c(t) is reaching to negative, as
> far as I know it can not be
> negative as the probability can not be negative.......please suggest
> where is the problem......
> 
> -- 
> -----------------------
> Thanks and Regards,
> Bipin Singh
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-----------------------------------------------
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
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html