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... On Thu, May 17, 2012 at 4:16 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thank you. Is it possible that this is caused by the trapped molecules > inside my tube? My tube ends are on the box edges so water cannot migrate > outside the tube where are the other water molecules. > > Steven > > > On Thu, May 17, 2012 at 3:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/17/12 10:38 AM, Steven Neumann wrote: >> >>> Well, I am still getting the same error when I try to do minimization: >>> "water >>> molecule on atom X cannot be settled" - these water molecules are not >>> close to >>> the Tube surface. If I will remove them the same error will occur but on >>> the >>> other atoms. If I specified only vdwradii for my Tube atoms why in the >>> bulk of >>> water there are some overlaps? Can you please help? >>> >>> >> The problem is not necessarily with the water molecule, but is more often >> indicative of some other instability in the system, such that forces are >> transmitted to that poor unsuspecting water molecule and it blows up. >> >> http://www.gromacs.org/**Documentation/Errors#LINCS.** >> 2fSETTLE.2fSHAKE_warnings<http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings> >> >> It's hard to diagnose, so make sure you're EM step is very small and you >> save configurations frequently in order to diagnose what's happening. It >> could be a problem with the .mdp file, topology, or perhaps some weird >> water overlap, but if that's the case, then genbox didn't do it, something >> else caused it. >> >> -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<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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