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

[Thereza Soares]

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.


I would appreciate any suggestions on what maybe wrong here,

Cheers,

Thereza

integrator               = md
dt                       = 0.002
nsteps                   = 25000000
nstxout                  = 500
nstvout                  = 500
nstlog                   = 500 
nstenergy                = 500
nstxtcout                = 500
comm-mode                = Linear
nstcomm                  = 5
comm-grps                = SYSTEM  
xtc_grps                 = SYSTEM
energygrps               = SYSTEM
nstlist                  = 5
rlist                    = 1.4
coulombtype              = generalized-reaction-field
epsilon_rf               = 66.0
ns_type                  = grid
rcoulomb                 = 1.4
rvdw                     = 1.4
pbc                      = xyz
tcoupl                   = berendsen
tc-grps                  = SYSTEM
tau_t                    = 0.2 
ref_t                    = 300 
Pcoupl                   = berendsen
Pcoupltype               = semi-isotropic
tau_p                    = 0.4 0.4 
compressibility          = 4.5e-5 4.5e-5 
ref_p                    = 1.0 1.0
gen_vel                  = yes 
gen_temp                 = 10
gen_seed                 = 178296
constraints              = h-bonds
disre             = simple
disre-weighting   = equal
disre-mixed       = no
disre-fc          = 1000
disre-tau         = 0
nstdisreout       = 1