[gmx-developers] unintended fatal error and pull code

Alan Chen alan.robot at gmail.com
Fri Dec 9 05:34:04 CET 2011

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

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


Alan Chen

chena7 at rpi.edu
Postdoctoral Fellow
Garcia Group
Biotech 2nd Floor RM 3237
Rensselaer Polytechnic Institute
110 8th Street
Troy, NY 12180

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