Re: how work: harmonic position "constraints" module + "WrapAll on"?

From: Joshua Adelman (
Date: Mon Jul 20 2009 - 09:23:13 CDT

Hi Sebastian,

The 'wrap' commands should only impact the way the outputs are
written. As far as I can tell from the description of your problem,
the constraints should work correctly. The thing to do to make sure
everything is working as you expect is to either:
1. Run a small test system and look at the distribution of the ion
position and see if it looks like you would expect. You can do this in
vacuum, so it would take very little time to test.
2. Look at the code to see if NAMD is wrapping the forces (or more
likely just the positions); The code in this section is fairly well
commented so it shouldn't be difficult to follow what is going on.

Best of luck,


On Jul 20, 2009, at 5:12 AM, Sebastian Stolzenberg wrote:

> Dear All,
> How does the harmonic position "constraints" module (with "consref"
> and "conRef") deal with periodic conditions that use "WrapAll on"?
> Conceptionally, let us assume we have an ion very close to the box
> boundary, focusing on one dimension only:
> - box boundaries are $x-$a and $x, where $x and $a are positive floats
> - an ion has position $x-$eps, to which it is weakly harmonically
> "constrained" with 0<$eps<<$a.
> Now, let us assume, having ended a first run, whose final restart
> file is such that the ion is at $x-$a+$eps, the opposite side of the
> box.
> The next run has to use the original "consRef" file with the ion
> reference set to $x-$eps (see *note in the bottom).
> My question:
> In which direction does the "constraints" module "pull" the ion? Is
> it smart enough to pull it into the negative direction, or will it
> pull it into the positive direction?
> Many Thanks,
> Sebastian
> *note: I know that I could simply change my "consRef" file to the
> last restart file, but that would complicate the way my wrapper code
> works.

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