Thank you very much I understood completely Best On Sun, May 8, 2011 at 7:30 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Thank you for your complete explanation. >> Please let me discribe where is NPT.cpt comes from: >> >> Before doing Pulling step,I did an NPT step (as your tutorial) to generate >> NPT ensemble. >> the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ... >> >> Then I used NPT.gro for Pulling step to generate config0.gro and ... >> >> After this step I used the NPT.cpt and config0.gro and .... to generate >> umbrella0.tpr with grompp. >> I think it is obvious now ,where is NPT.cpt come from! >> >> I think my mistake is as you noted.I didn't use any -t option in >> grompp,Then I lost the information for npt ensemble. >> >> What do you think >> > > The pre-SMD NPT ensemble has nothing to do with any of the configurations > generated during SMD. The coordinates and ensemble information in NPT.cpt > reflect the position-restrained system prior to the application of the > steering force. > > You should not use this NPT.cpt file for anything after SMD. I explained > an appropriate workflow in my last message. > > > -Justin > > -- > ======================================== > > 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 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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