On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth <katesed...@gmail.com> wrote:
> Hi Vitaly, > > I realize that when one extends the Z direction the resulting interface is > liquid-vacuum, but I see that even at T below boiling point some molecules > still leave the interface and enter the empty zone and are added to the > other side due to PBC. as a result the density profile does not exactly go > down to zero but tends to zero anyways. I was wondering if this is > considered a liquid-vapor interface? > YES > or it is still liquid-vacuum? > > thanks! > > > On 1 April 2013 14:43, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > >> There is a wonderful data page devoted to methane in wikipedia... >> >> It follows from this webpage that you will get a perfect density profile >> if you decrease your T down to 150K... >> >> >> On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: >> >>> >>> >>> >>> On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth <katesed...@gmail.com> wrote: >>> >>>> You are right. I compressed my alkane system under NPT at 400 K at 100 >>>> bar. The normal boiling point is below 425 K. So it seems there in no way >>>> one can obtain profiles obove boiling point of liquid given than with the >>>> current NVT recipe molecules tend to fill up the free zone no matter how >>>> much pressure was applied in the previous NPT runs? >>>> >>>> >>> >>> You cannot get a profile just because you have NO LIQUID and NO >>> INTERFACE upon these conditions. Gas fills all the available space, there >>> is no such thing as gas/gas interface. >>> >>> And yeah... Forget about NPT and learn the Gibbs phase rule. >>> >>> >>> Dr. Vitaly Chaban >>> >>> >>> >>> >>> >>> >>>> >>>> On 1 April 2013 14:22, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: >>>> >>>>> >>>>> >>>>> >>>>> On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth <katesed...@gmail.com>wrote: >>>>> >>>>>> 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? >>>>>> >>>>>> >>>>> >>>>> Here we come to the question what your system is composed of... Based >>>>> on the density profile, this is not a (conventional) liquid... Polymer, >>>>> non-Newtonian liquid ... or what? >>>>> >>>>> If molecules tend to fill vacuum, it can only mean that the matter you >>>>> are simulating is above critical point. >>>>> >>>>> What is your T and what are the particles in your box? >>>>> >>>>> >>>>> Dr. Vitaly Chaban >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> 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