On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > On 5/17/12 11:50 AM, Steven Neumann wrote: > >> My tube is finite. I increased my box so the water could interact with >> all water >> molecules. The same problem: My minim.mdp >> >> ; minim.mdp - used as input into grompp to generate em.tpr >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 10.0 ; >> emstep = 0.001 >> nsteps = 50000 ; Maximum number of (minimization) steps to >> perform >> nstxout = 1 >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list and long >> range forces >> ns_type = grid ; Method to determine neighbor list (simple, >> grid) >> rlist = 1.4 ; Cut-off for making neighbor list (short range >> forces) >> coulombtype = PME ; Treatment of long range electrostatic >> interactions >> rcoulomb = 1.4 ; Short-range electrostatic cut-off >> rvdw = 1.4 ; Short-range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions (yes/no) >> >> Well... no clue... >> >> > Then the diagnostic tips I listed before still apply, as well as those > listed on the webpage linked from what I posted earlier. > > > -Justin > Thank you Jusin! By the way, how can I create infinite tube in gmx? > > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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