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
