Re: minimizer slowly moving atoms with bad contacts downhill

From: Axel Kohlmeyer (
Date: Fri Apr 12 2013 - 03:56:19 CDT

On Fri, Apr 12, 2013 at 9:02 AM, Himani Raina <> wrote:
> hello
> I am trying to minimze a membrane protein alone without the solvent for 1000
> steps and when I open the log file I get the error minimizer slowly moving
> "n" atoms with bad contacts for the first 25 steps and it shows different
> value for n each time . I tried doing the minimization at 10000 steps also
> same error was reported. and when I further did equilibration error was
> atoms moving too fast .
> Please help me in this matter .

this is a common problem. you can research the mailing list archives
for lots of advice on that.

you have close contacts, i.e. some atoms are overlapping too much. you
need to check your structure and perhaps manually move atoms apart a
little bit. please also check you definition of the simulation cell.
that can result in overlaps as well due to periodic boundaries.


> --
> Thanks And Regards
> Himani Raina

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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