From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Tue Apr 05 2016 - 10:18:25 CDT
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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