How about it that I get a positive potential energy for a system of only protein and POPC? Makes sense?
Thanks for your explanation. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Wednesday, December 12, 2012 4:11 PM Subject: Re: [gmx-users] Re: Poteintial energy of my system On 12/12/12 5:16 AM, Shima Arasteh wrote: > > > What are the possible solutions to solve the problem? > > My system is composed of protein, POPC, ions, and water. I follow the > approached suggested in kalp15-DPPC tutorial. > And I got such an incorrect potential for the first grompp. > Would you please guide me? > > I would appreciate ur suggestions. > The outcome is rather puzzling. Fmax indicates the system should be happy, but the potential is clearly not. A positive potential indicates net repulsion and/or unsatisfied interactions, which should not happen for a condensed phase system. In vacuo, positive potentials are more common (depending, of course, on what the system is). Check for voids in the unit cell. That's about the only thing I can think of. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
