From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Apr 05 2016 - 10:10:44 CDT
Hi Farideh,
I have encountered this problem multiple times, usually due to the periodic
box not set correctly. I am not familiar with your system (i.e. the
dendrimer), but how did you specify the cellBasisVectors? How did you
calculate your PBC dimensions? That might be an issue.
Best,
Chitrak.
On Tue, Apr 5, 2016 at 10:57 AM, faride badalkhani <
farideh.khamseh_at_gmail.com> 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
>
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