Constraint failure in RATTLE algorithm for atom 538

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Tue Apr 05 2016 - 09:57:30 CDT

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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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