Hello all I had simulated Tip4p-2005 water system with different concentrations of MgCl2 and Cacl2 salts. I have calculated the Surface tensions of the systems and I see that presence of the salt increases the S.T of water layer. Now to do more analysis i want to calculate the contributions of water and ions to the electrostatic potential . I should use g_potential command. I need an index file. Do I need to specify water, Mg and Cl groups in the index file? is this command format corect? g_potential -f traj.trr -n index.ndx -s topol.tpr ? Please let me know if I should consider anything else? thanks Regards D.Aghaie
--- On Fri, 5/13/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] pressure in NPT and NVT To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Friday, May 13, 2011, 5:36 PM Nilesh Dhumal wrote: > Hello, > > I am using NPT simulation for water - spce model (opls-aa force field). > I have the reference pressure set at ref_p = 1.0 bar. > I checked the average pressure using g_energy and it is 2.81972 bar. > > Why there increase in pressure? > > Probably the system is not yet equilibrated. > > For NVT simulatin I get the value around average pressure 710.685 bar. > > I am running the simulation at 295 k and average temp. is 294.98 K which > look ok. > > > Can you tell why there is increase in pressure for NPT and why there is > so high value of pressure in NVT. > Because the box is fixed. It cannot respond to internal forces in your system. Pressure values during NVT don't mean much. -Justin > I am using gromacs version 4.0.7. > > Thanks > > Nilesh > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
-- 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
