my starting structure has just two atoms one Na and one Cl and they are seperated by a distance of 3 angstroms.Its not a huge system.
On Sun, May 22, 2011 at 10:30 AM, Mark Abraham <[email protected]>wrote: > On 22/05/2011 2:43 PM, sreelakshmi ramesh wrote: > > Dear gmx-users, > I have a problem during minimization and shows > a error that water molecules starting at atom X cannot be settled i had > attached the output of mdrun below. I read the earlier post for same problem > faced by other gmx users.tried to reduce the timestep still facing the same > error.Tried diff water model and force fields as well to check if i get the > same error .But still irrespective of any water model and forcefield i get > the same error.And was not able to find a solution.Any suggestion > please.... > > > Several people have suggested you may have a bad starting structure, with > atoms overlapping or such. This confirms it. > > Mark > > > *OUTPUT OF MDRUN* > > Back Off! I just backed up md.log to ./#md.log.1# > Reading file em.tpr, VERSION 4.5.3 (single precision) > Starting 2 threads > Making 1D domain decomposition 2 x 1 x 1 > > Back Off! I just backed up em.trr to ./#em.trr.1# > > Back Off! I just backed up em.edr to ./#em.edr.1# > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+02 > Number of steps = 200000 > > step 7: Water molecule starting at atom 7619 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > step 7: Water molecule starting at atom 3547 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > > step 12: Water molecule starting at atom 7619 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > > step 17: Water molecule starting at atom 8007 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > > step 22: Water molecule starting at atom 8511 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 100 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Back Off! I just backed up confout.gro to ./#confout.gro.1# > > Steepest Descents converged to machine precision in 40 steps, > but did not reach the requested Fmax < 100. > Potential Energy = 2.4059008e+07 > Maximum force = 2.8605226e+08 on atom 8511 > Norm of force = 3.7174682e+06 > > gcq#324: "Your Country Raised You, Your Country Fed You, and Just Like Any > Other Country it Will Break You" (Gogol Bordello) > > > > -- > 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 >
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