[gmx-developers] unintended fatal error and pull code
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Fri Dec 9 16:28:24 CET 2011
That sounds like a pretty serious error. I checked the redmine report.
Are you sure that this would lead to visible artefacts or crashes? It
doesn't take too many highly non-boltzmann sampling values to totally
change a PMF.
Sorry to hijack the original post, I realize that the original
question has not been answered yet.
Quoting Berk Hess <hess at kth.se>:
> There is a bug in this distance check. It should check dr[m]*dr[m],
> not dr[m].
> 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
>> 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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