Re: problems running ABF simulation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Sep 02 2014 - 02:45:26 CDT

Hello Charles, I think it's safe to say that while there is no problem
defining 15 colvars, it's much more difficult to store a 15-dimensional
grid of forces and energy values.

Giacomo
On Sep 2, 2014 7:39 AM, "Charles Whidborne" <
charles.whidborne_at_student.adelaide.edu.au> wrote:

> Hi,
>
> I am trying to run an ABF simulation in which i have defined 15 colvars
> along a DNA strand, but each time i submit it it comes up with the same
> error message which i don't understand.
> The message is:
> terminate called after throwing an instance of 'std::length_error'
> what(): vector::reserve
> Abort
>
> The only thing i can attribute it to is the Distance.in input file for the
> ABF.
> Is it possible that i have defined too many Colvars? i have 15 all up
> (colvars = { COMDistance1, COMDistance2, COMDistance3, COMDistance4,
> COMDistance5, COMDistance6, COMDistance7, COMDistance8, COMDistance9,
> COMDistance10, COMDistance11, COMDistance12, COMDistance13, COMDistance14,
> COMDistance15 }) This line appears in the output log file, so i assumed
> that namd was handling them all okay, but terminates after this
> 'initializing ABF' section.
> I have tried renaming each of the colvar 1, 2, 3... 15 to shorten the
> line, but i still encounter the same problem.
>
> Any help would be appreciated.
>
> Thanks,
>
> Charlie
>

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