**From:** Olya Kravchenko (*ovkrav_at_gmail.com*)

**Date:** Tue Apr 05 2016 - 10:29:38 CDT

**Next message:**Chitrak Gupta: "Re: Constraint failure in RATTLE algorithm for atom 538"**Previous message:**faride badalkhani: "Re: Constraint failure in RATTLE algorithm for atom 538"**In reply to:**faride badalkhani: "Re: Constraint failure in RATTLE algorithm for atom 538"**Next in thread:**Chitrak Gupta: "Re: Constraint failure in RATTLE algorithm for atom 538"**Reply:**Chitrak Gupta: "Re: Constraint failure in RATTLE algorithm for atom 538"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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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