[gmx-users] Water molecule starting at atom X can not be settled.
Mark Abraham
Mark.Abraham at anu.edu.au
Sun May 22 09:27:44 CEST 2011
On 22/05/2011 4:54 PM, sreelakshmi ramesh wrote:
> ya sorry i actually meant to say that the starting pdb file had just
> NA and Cl.I then solvated it with tip4p water.Anad then try to
> minimize it.
Then you must have done it wrong. Follow along the workflow of a
tutorial. Maybe your ion atom types do not match the names in the VDW
radii database and that is generating atom clashes. See genbox -h
When asking for help give complete descriptions and exact commands
copied from your terminal. Nobody's got the time to solve your problem
except you, but if you want someone else's insight for free, you need to
give them all the data you think might even possibly be relevant. They
aren't going to bother asking questions to get data that you could have
already provided...
Mark
> On Sun, May 22, 2011 at 11:59 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> 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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>
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