[gmx-users] Comparing MD ensembles with exp. NOE restraints --> bus error

[Justin A. Lemkul]

Thereza Soares wrote:
> Hi There,
> 
> I would like to compare my ensemble of (unrestrained) MD structures against
> experimental NOE distances. For that, I have added the distance_restraints
> block to my *.top file such as:
> 
> [distance_restraints] 
 > ;ai    aj type index type’ low   up1 up2 fac
 > 33    31    1    0    1  0.0  3.000 1.2 0.4
 > 35    31    1    1    1  0.0  2.500 0.7 0.3
> 
> 
> I have also added the disre options below to the *.mdp file used to generate
> a new tpr for the NOE analysis
> 
> disre             = Simple 
 > disre-weighting   = Equal
 > disre-mixed       = no
> disre-fc          = 1000 
 > disre-tau         = 0
 > nstdisreout       = 1
> 
> When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives
> a bus error ... I am copying the entire mdp file in case someone can point me
> out what is wrong with it.
> 

There is nothing wrong with the .mdp file.  There is likely a bug in the g_disre 
code somewhere, as is usually the case with immediate bus errors or segmentation 
faults.

> 
> I would appreciate any suggestions on what maybe wrong here,
> 

You haven't mentioned which version of Gromacs you're using, but if it is not 
4.5.4 (the latest), please try again with this version.  If you are using 4.5.4 
or the error persists, please file an issue report on redmine.gromacs.org and 
include your .tpr and .pdb files necessary to reproduce the problem.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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