Hi Vitaly, The problem was with cpt file since it re sets the last line of gro. I removed the -f flag and now the Z direction is extended. However, I see that molecules tend to fill up the upper zone (free space) rapidly. I am wondering how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run?
I am expecting to see how density changes with Z at the solvent -vacuum interface.... Please advise me on this,, Thanks! On 1 April 2013 13:14, 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. > > > 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
