Re: Constraint failure in RATTLE algorithm for atom 538

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Apr 05 2016 - 10:29:38 CDT

Faride,

can you post your configuration file as well as the output of the
measure minmax command?

On Tue, Apr 5, 2016 at 11:18 AM, faride badalkhani
<farideh.khamseh_at_gmail.com> wrote:
> I had a plan to heat the system like:
> 1) 0 to 100 K
> 2) 100 to 200 K
> 3) 200 to 298 K
>
> But at the first step (i.e. 0 to 100 K) I got the same error.
>
> Regards,
> Farideh
>
> On Tue, Apr 5, 2016 at 11:04 AM, Brian Radak <bradak_at_anl.gov> wrote:
>>
>> I wouldn't recommend minimizing that much. Personally I never exceed 1000
>> steps.
>>
>> You might be getting an error from PBCs, so maybe check the box dimensions
>> (i.e. set them larger and try to repeat the calculation)?
>>
>> You can also try heating gradually with an annealing protocol starting at
>> low temperature and then ramping up.
>>
>> Brian
>>
>>
>> On 04/05/2016 09:57 AM, faride badalkhani wrote:
>>
>> Dear all,
>>
>> I want to perform a simulation on a system includes a dendrimer
>> (hyperbranched polymer) in water. I built the pdb structure by GaussView
>> software and then wrote a tcl command to patch residues together. When I
>> build the psf executing tcl command there is no error and everything seems
>> correct. But, when I minimize the system exactly after minimization and
>> before NVT equilibration starts I get this error.
>> ERROR: Constraint failure in RATTLE algorithm for atom 179!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Exiting prematurely; see error messages above.
>> ====================================================
>>
>> WallClock: 1845.095215 CPUTime: 1845.095215 Memory: 181.218750 MB
>> ERROR: Constraint failure in RATTLE algorithm for atom 538!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 13!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1095!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 748!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 149!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 349!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 315!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 210!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 84!
>> ERROR: Constraint failure; simulation has become unstable.
>> [Partition 0][Node 0] End of program
>>
>> I took a look at namd mailing list and I decreased the timestep and
>> increased the minimization from 20000 to 50000 but it did not work for me. I
>> really need your help, because I do not know what is the problem.
>>
>> Regards,
>> Farideh
>>
>>
>> --
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
>> brian.radak_at_anl.gov
>
>

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