I think if you use checkpoint files, the program does not read either MDP, or GRO, or TOP, or anything except CPT.
Dr. Vitaly Chaban On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth <katesed...@gmail.com> wrote: > Hi vitaly, > > The initial structure is indeed extended but the final output.gro is not. > I think its because I am using the cpt file from the previous NPT runs as > input for the new runs? Do I have to remove the -t flag? > > > On 1 April 2013 12:47, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > >> Hi Elisabeth - >> >> The only explanation is that you actually DID NOT extend the box in Z >> direction. Look at the last line of confout.gro. >> >> g_density -d Z gives you a [local] density versus Z coordinate. >> >> >> Dr. Vitaly Chaban >> >> >> >> >> On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth <katesed...@gmail.com> wrote: >> >>> Hi Vitaly, >>> >>> I did NVT simulations and tried to obtain density profile at interface >>> along Z using g_density -f .trr -s .tpr -d Z but I what I see is the >>> density profile in the box not the interface. Box size is 3 nm and Before >>> NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! >>> >> >> > -- 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
