On Fri, May 18, 2012 at 12:20 PM, Justin A. Lemkul <[email protected]> wrote:
> > > On 5/18/12 6:58 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> My system consists of a Tube made of Oxygen, Hydrogen and ions. These >> atoms are >> not connected via bonds. I try tu run EM: >> >> ; 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 = 1000.0 ; Stop minimization when the maximum force < >> 1000.0 >> kJ/mol/nm >> 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) >> >> freezegrps = TUB >> freezedim = Y Y Y >> >> >> Then a lot of errors "water molecule on atom X cannot be settled". I >> tried: >> >> 1. constraints = none >> >> 2. remove those water molecules - then other water molecules have the >> same error >> >> 3. using nstxout =1 in VMD, I could observe that some of the molecules >> facing >> this error split in one frame (hydrogens 7A away from oxygen) or spin >> around 180 >> degrees - it depends. >> >> 4. I tried increase vdwradii of the atoms which form my Tube so they wont >> overlap with water >> >> >> If you have any suggestions I will really appreciate, >> >> > This is starting to sound more and more like a topology instability. Can > you successfully run EM on your tube in the absence of water? If not, then > the problem is with the definition of the tube, with the water problems > being a consequence. > > -Justin > > Thank you. I tried without water and it works really fine. However, the posted mdp with water was with the emtol = 1000 - then NO errors occur. When I decrease it to 100 then this error appears. I will try to process it to NVT and see how it goes. > -- > ==============================**========== > > 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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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