[gmx-developers] unintended fatal error and pull code

Berk Hess hess at kth.se
Fri Dec 9 10:43:57 CET 2011


There is a bug in this distance check. It should check dr[m]*dr[m], not 
Two weeks ago I filed an issue and fixed it for the upcoming 4.5.6:


On 12/09/2011 05:34 AM, Alan Chen wrote:
> Hi all:
> I just wanted to report what I thought was an overly restrictive fatal
> error case in the 4.5.5 pull code. Previously, I've been very happily
> simulating an optical-tweezers type dissociation experiment (i.e.
> non-equilibrium pulling) using version 4.0.5 where I have a
> bimolecular complex in solvent aligned in a long, narrow box that I
> dissociate by applying a constant force to two atoms on opposite ends
> of the complex (i.e. two pull groups pulled in opposite directions
> along the long box dimension).  This is ideal, as the actual single
> molecule experiment I'm comparing to applies a constant force to two
> tethered groups of an aligned complex (albeit at a much longer
> timescale).
> Upgrading to 4.5.5 I found my simulations quickly aborted with the
> error "Fatal error:
> Distance of pull group 2 (2.687620 nm) is larger than 0.49 times the
> box size (7.520599)"
> searching the code referenced in the error message, I see this line
> was tripped in pull.c
>   if (max_dist2>= 0&&  dr2>  0.98*0.98*max_dist2)
>      {
>          gmx_fatal(FARGS,"Distance of pull group %d (%f nm) is larger
> than 0.49 times the box size (%f)",g,sqrt(dr2),max_dist2);
>      }
> Now this sanity check makes sense if I was applying a distance-based
> bias, as the minimum distance vector will abruptly shift to one of the
> periodic images and not do what you would intuitively want a
> distance-based bias to do. However, in my case of simulating a force
> microscopy style experiment with constant force along the Y axis there
> is nothing wrong with having such widely separated pull groups.  For
> my own purposes, I can easily just comment out this line and recompile
> but I just wanted to suggest that maybe in future versions this error
> should only be tripped if there is a distance-based bias being
> invoked?
> Cheers,
> Alan Chen
> chena7 at rpi.edu
> Postdoctoral Fellow
> Garcia Group
> Biotech 2nd Floor RM 3237
> Rensselaer Polytechnic Institute
> 110 8th Street
> Troy, NY 12180

More information about the gromacs.org_gmx-developers mailing list