[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>:

> Hi,
> 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:
> http://redmine.gromacs.org/issues/844
> Berk
> 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
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list