Re: [gmx-users] data.xvg for g_kinetics ?
On 2010-09-24 23.31, Justin A. Lemkul wrote: feng chen wrote: Hi gromacs user, We recently ran in this problem when try to analyise our REMD trajectories. g_kinetics module will be used for such kinda analysis, however it looks like we need provide 2 xvgs file as input. The temp.xvg we can get from demux.pl http://demux.pl and the other one (data.xvg) we are not sure how to get . To get a better understanding of this g_kinetics module, we have read through that reference paper, but throught the that whole paper (Phys. Rev. Lett. 96, http://dx.doi.org/10.1103/PhysRevLett.96.238102) there's no hint about how to prepare this data.xvg file. So, we were wondering , can anybody kindly let us know how did u guys get this data.xvg file? The content of the second input file is dependent upon how you assess folding. The paper you reference, IIRC, used RMSD as this indicator. In principle, you should be able to use other metrics like R(g), native contacts, etc. That's correct, and the RMSD is quantized by setting the cut-off value. -Justin thanks a lot Kevin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
[gmx-users] data.xvg for g_kinetics ?
Hi gromacs user, We recently ran in this problem when try to analyise our REMD trajectories. g_kinetics module will be used for such kinda analysis, however it looks like we need provide 2 xvgs file as input. The temp.xvg we can get from demux.pl and the other one (data.xvg) we are not sure how to get . To get a better understanding of this g_kinetics module, we have read through that reference paper, but throught the that whole paper (Phys. Rev. Lett. 96, http://dx.doi.org/10.1103/PhysRevLett.96.238102) there's no hint about how to prepare this data.xvg file. So, we were wondering , can anybody kindly let us know how did u guys get this data.xvg file? thanks a lot Kevin -- gmx-users mailing listgmx-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
Re: [gmx-users] data.xvg for g_kinetics ?
feng chen wrote: Hi gromacs user, We recently ran in this problem when try to analyise our REMD trajectories. g_kinetics module will be used for such kinda analysis, however it looks like we need provide 2 xvgs file as input. The temp.xvg we can get from demux.pl http://demux.pl and the other one (data.xvg) we are not sure how to get . To get a better understanding of this g_kinetics module, we have read through that reference paper, but throught the that whole paper (Phys. Rev. Lett. 96, http://dx.doi.org/10.1103/PhysRevLett.96.238102) there's no hint about how to prepare this data.xvg file. So, we were wondering , can anybody kindly let us know how did u guys get this data.xvg file? The content of the second input file is dependent upon how you assess folding. The paper you reference, IIRC, used RMSD as this indicator. In principle, you should be able to use other metrics like R(g), native contacts, etc. -Justin thanks a lot Kevin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
