Thanks alot Negar!! I am going to try, I'll ask you if I face with a problem.
Best regards On Wed, Apr 6, 2016 at 5:09 PM, Negar Ashari Astani <negarast...@gmail.com> wrote: > ... Yes, I guess this can be easily done using Density profile tool of > VMD. Since you are running classical simulations with gromacs you probably > have your system topology with different residues and fragments. So you can > easily choose each phase of your system in selected atoms (a combination of > residues) and ask for the the density of this phase in the course of > simulation. You just need to be careful when converting the units, as this > plugin counts the atoms, thus if you have water molecule, the plugin counts > that molecule three times (three atoms of the molecule), so you need to put > "Name O and residue WAT" such that it counts a water molecule only once! > > Let me know if you need more explanation, > Best, > Negar > > On Wed, Apr 6, 2016 at 4:59 PM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > >> Thanks Negar. >> >> More detail; my system phase-separate after equilibrium, such that each >> component reaches two mole (or mass) fractions. One mole fraction at its >> rich-phase and one mole fraction at its poor phase. I need to know those >> two densities or fractions. >> >> I do not know your way. Could you explain me a bit more. >> >> >> Best regards >> >> >> On Wed, Apr 6, 2016 at 4:45 PM, Negar Ashari Astani < >> negarast...@gmail.com> wrote: >> >>> .... Just a correction: The main plugin I used is " Density profile >>> tool" and then for visualization as a volumetric density I used VOLMAP. >>> >>> On Wed, Apr 6, 2016 at 4:42 PM Negar Ashari Astani < >>> negarast...@gmail.com> wrote: >>> >>>> Hello Faezeh, >>>> >>>> If by density you mean the mass density, you can use VOLMAP plugin of >>>> VMD to analyze the density evolution in the course of simulation. >>>> If this is what you mean, I'll be happy to help with more information. >>>> >>>> Best, >>>> Negar >>>> >>>> >>>> On Wed, Apr 6, 2016 at 4:30 PM Faezeh Pousaneh <fpoosa...@gmail.com> >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> Is it possible to obtain partial density versus time in Gromacs? >>>>> Precisely, >>>>> I have a system of two components which separate by time. I need the >>>>> evolution of density of each phase by time? >>>>> >>>>> thanks. >>>>> Best regards >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>> >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.