On 10 September 2011 18:03, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Juliette N. wrote: > >> Hello, >> >> I am trying to extend a simulation to 2 ns and wanted to know if I am >> using the proper tools for this purpose. (version 4.5.4) >> >> 1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000 >> >> mdrun -s old-extend.tpr -cpi old.cpt -o old-extend -c old-extend -e >> old-extend >> >> Is what I am doing correct? >> >> > Yes. Save yourself some typing with: > > mdrun -deffnm old-extend -cpi old.cpt > > > 2) Can I use the following in 4.5.4 instead of above? >> >> mdrun -s old.tpr -cpi old.cpt -append 2000 >> >> > No. The mdrun -append option does not take an argument; it is a boolean > (i.e. -append/-noappend) to indicate whether old files are to be appended to > or not. > Thank you. Where can I define how long simulation is going to be? I think the advantage of append is that it combines old and old-extend energy files and there is no need for eneconv -f old-extend.edr old.edr -o concatenate2ns.edr Is that right? I am just trying to get the most of the tools and skip unnecessary tools like eneconv as far as it is possible.I am a little confused as there are different ways explained on "doing restarts" page. tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000 mdrun -deffnm old-extend -cpi old.cpt does this concatenate energy files? > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Thanks, J. N.
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