**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

**Next message:**Nicholus Bhattacharjee: "Few doubt on the numbers implying in REMD simulation"**Previous message:**Brian Radak: "Re: AW: AW: AW: why does the transition seem to be irreversible in aMD"**Next in thread:**Brian Radak: "Re: Constraint failure in RATTLE algorithm for atom 538"**Reply:**Brian Radak: "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 ]

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