[gmx-users] Water molecule starting at atom X can not be settled.

[Mark Abraham]

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)
>

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