Re: [NAMD] Too many collective variables?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Oct 26 2017 - 15:34:51 CDT

Hi, how big is the file separation.in and what is the software
environment? Each file is cached into a string. The maximum size is given
by the C++ library, but that limit is quite big (usually 4 GB).

I sure hope that you're generating that file with a loop and not manually.
If it helps, know that you can break the configuration in multiple chunks
and load them using "cv configfile" or give the definitions inside the NAMD
script itself:

for { set i 0 } { $i < MAX } { incr i } {
  cv config "
colvar {
    name d$i
    ...
}"
}

On Thu, Oct 26, 2017 at 4:11 PM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> Hi everyone,
>
> I'm running a simulation where I pull a molecule from 257 different places
> simultaneously. So far I haven't had problems using 201 and 207 places,
> but when I use 257 it seems like my code starts at 158:
> colvars: Reading new configuration from file "separation.in":
> colvars: # indexFile = "" [default]
> colvars: # smp = on [default]
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 100 [default]
> colvars: # colvarsRestartFrequency = 100000 [default]
> colvars: # colvarsTrajAppend = off [default]
> colvars: # scriptedColvarForces = off [default]
> colvars: # scriptingAfterBiases = on [default]
> colvars: ------------------------------------------------------------
> ----------
> colvars: Initializing a new collective variable.
> colvars: # name = "d158"
> ...
> colvars: ------------------------------------------------------------
> ----------
> colvars: Collective variables initialized, 103 in total.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = "harmonic1" [default]
> colvars: # colvars = { d1 }
> colvars: Error: cannot find a colvar named "d1".
> FATAL ERROR: Error in the collective variables module: exiting.
>
>
> Is there a maximum for the number of collective variables? Any idea of how
> can I avoid this problem or why could it have happened?
>
> Thanks!
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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