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

[Mark Abraham]

On 22/05/2011 3:35 PM, sreelakshmi ramesh wrote:
> 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.

So how come you have water molecules?

Mark

>
> On Sun, May 22, 2011 at 10:30 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> 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)
>>
>
>
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