Re: ABF/colvar error in NAMD2.9

From: Aron Broom (
Date: Tue Jul 22 2014 - 12:32:06 CDT

Jerome: You are certainly correct, I hadn't thought is was a single
massively-dimensional bias. The memory thing makes much more sense now, as
per your equation.

Harish: Memory issues aside then, I don't think you would ever be able to
reach equilibrium with such a massive coordinate space to bias across. If
you look at Jerome's equation it not only relates to memory usage, but is
also proportional to how many timesteps you would need to sample
everything. The unfortunate truth is that given current technology, brute
forcing a problem like this (trying to explore over all the conformations)
just isn't possible. You need to do something that is less explicit in
it's biasing, like replica exchange or some other form of accelerated
sampling that doesn't require the full exploration of the coordinate space.

On Tue, Jul 22, 2014 at 12:56 PM, Jérôme Hénin <> wrote:

> Aron, when you ahd 9 colvars, maybe they were not assigned a single ABF
> bias?
> On 22 July 2014 18:30, Aron Broom <> wrote:
>> I've used an upwards of 9 colvars at once with no issue, and with a
>> larger system size than that. Can you post the *.in file or whatever file
>> contains all your colvars definitions? I would suspect something add with
>> your colvars. One thing to test might be, when you are at the largest size
>> that has worked (I guess 4 colvars?) try just duplicating all those colvar
>> blocks and see if it runs. Maybe something is wrong with the 5th colvar
>> definition you are entering.
>> On Tue, Jul 22, 2014 at 12:23 PM, Harish Vashisth <
>>> wrote:
>>> Dear All:
>>> We have been trying to make use of many CVs (> 20) using abf/colvar
>>> options in NAMD2.9. These are all backbone dihedral CVs defined
>>> individually in multiple blocks of phi/psi, etc. We are able to run ABF
>>> jobs fine up to 5 CVs, but including a sixth one or more does not work. The
>>> error reported in the log file right after initialization of colvars module
>>> is:
>>> FATAL ERROR: Memory allocation failed on processor 0.
>>> Looking through previous posts, someone seemed to suggest that it is
>>> likely occurring due to large system size as NAMD keeps a copy of the
>>> system on processor 0?
>>> In our case, the solvated system size is ~40,000 atoms. The error occurs
>>> using NAMD2.9 on local workstation, our local CRAYXE6m-200 as well as on
>>> Stampede (XSEDE resource.) Is there an upper limit on how many CVs colvar
>>> module can handle?
>>> Any suggestions would be helpful. Thanks.
>>> -Harish
>>> --------------
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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