From: Brian Radak (bradak_at_anl.gov)
Date: Tue Apr 05 2016 - 10:04:40 CDT
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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