Ah. -666 is used whenever the sitting of the kinetic model fails to converge. This is a poor way of signalling that something went wrong that should be changed. Again, did you *look* at the acf?
Erik 30 mar 2012 kl. 11.53 skrev Nidhi Katyal: > for another system (at 250K) also i have calculated hydrogen bond lifetime > using: > hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250 > whose output is : > acf 14477/14477 > normalization for c(t)=0.0135742 for gh(t)=6.78702e-05 > hydogen bond thermodynamics at T=250K > fitting parameters chi^2 = 3.89447e-06 > Type rate time DG chi^2 > forward -1.201 -0.833 -666.000 3.89447e-06 > backward -0.354 -2.823 -666.000 > ...... > > Here again i am getting negative hydrogen bond lifetime. > Please suggest me where i am getting wrong and what does negative lifetime > mean? > Thank you in advance. > > > On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund <[email protected]> wrote: > > 29 mar 2012 kl. 18.47 skrev Nidhi Katyal: > >> Dear All >> I would like to know the strength of the given bond by calculating the >> lifetime of that bond.For the same reason i used: >> g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg >> and i got: >> Type Rate(1/ps) Time(ps) ... >> Forward -0.182 -5.495 >> ....... >> HB lifetime=50.60ps >> Note that the lifetime obtained in this manner is close to useless.Use the >> -ac option instead and check the forward lifetime. >> .. >> Will it be correct to say that lifetime is -5.495ps (looking at forward >> time)? But then what does negative lifetime implies? >> Thanks in advance. > > Seems weird. Could the amount of underlying data be insufficient? Have you > looked at the acf? > > Erik > >> -- >> 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > [email protected] > http://www2.icm.uu.se/molbio/elflab/index.html > > > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
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