From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Apr 05 2016 - 11:04:08 CDT
I am slightly confused by the order you mentioned. Did you do the minmax
before solvating? That's not what you should be doing. Make sure all your
solvation/ionization is done before you are getting the minmax output to be
used in cellBasisVector.
On Tue, Apr 5, 2016 at 11:29 AM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
> 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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