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