Justin - I am sure mdrun reads coordinates from -cpi state.cpt ....
Vitaly On Mon, Apr 1, 2013 at 7:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On Mon, Apr 1, 2013 at 1:29 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > >> It is something very new for me. >> >> If structure, etc are not read from CPT files, why does one need them >> for... >> > > I just tested and verified that -c is required, even in the presence of -t > passing a .cpt file. I suspect that the rationale is that the .cpt file is > used for state variables, velocities, etc (i.e. an upgrade over the very > old mechanism of passing a .trr to -t and .edr to -e). It would certainly > make sense if the coordinates from the .cpt were read, but I don't know if > doing so present a substantial improvement over using a coordinate file to > -c. > > -Justin > > >> >> > >> On Mon, Apr 1, 2013 at 7:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> >>> On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: >>> >>>> I think if you use checkpoint files, the program does not read either >>>> MDP, >>>> or GRO, or TOP, or anything except CPT. >>>> >>>> >>>> >>> I would have to check the code to be sure, but that is certainly not >>> true in the case of the .mdp file. That is always read. I want to say >>> that the coordinate file is required as well, though that would be an easy >>> test using grompp. It should be easy to track the box vectors from the >>> .edr file to see what the initial value was, to see if it came from the >>> .cpt or .gro file. Likely from the .cpt file. >>> >>> -Justin >>> >>> -- >>> >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) >>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> >>> >>> >> > > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://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