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 <er...@xray.bmc.uu.se>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 gmx-users@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-requ...@gromacs.org. > 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 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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